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Report on influenza viruses received and tested by the Melbourne WHO Collaborating Centre for Reference and Research on Influenza in 2019 - Report ...
2021              Volume 45
https://doi.org/10.33321/cdi.2021.45.43

Report on influenza viruses received and tested
by the Melbourne WHO Collaborating Centre for
Reference and Research on Influenza in 2019
Heidi Peck, Jean Moselen, Sook Kwan Brown, Megan Triantafilou, Hilda Lau, Miguel Grau, Ian G Barr,
Vivian KY Leung
Communicable Diseases Intelligence                                      Communicable Diseases Intelligence
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Annual report

Report on influenza viruses received and tested
by the Melbourne WHO Collaborating Centre for
Reference and Research on Influenza in 2019
Heidi Peck, Jean Moselen, Sook Kwan Brown, Megan Triantafilou, Hilda Lau, Miguel Grau, Ian G Barr, Vivian KY Leung

Abstract

As part of its role in the World Health Organization’s (WHO) Global Influenza Surveillance and
Response System (GISRS), the WHO Collaborating Centre for Reference and Research on Influenza
in Melbourne received a record total of 9,266 human influenza positive samples during 2019. Viruses
were analysed for their antigenic, genetic and antiviral susceptibility properties. Selected viruses
were propagated in qualified cells or embryonated hen’s eggs for potential use in seasonal influenza
virus vaccines. In 2019, influenza A(H3N2) viruses predominated over influenza A(H1N1)pdm09
and B viruses, accounting for a total of 51% of all viruses analysed. The majority of A(H1N1)pdm09,
A(H3N2) and influenza B viruses analysed at the Centre were found to be antigenically similar to the
respective WHO recommended vaccine strains for the Southern Hemisphere in 2019. However, phy-
logenetic analysis indicated that a significant proportion of circulating A(H3N2) viruses had under-
gone genetic drift relative to the WHO recommended vaccine strain for 2019. Of 5,301 samples tested
for susceptibility to the neuraminidase inhibitors oseltamivir and zanamivir, four A(H1N1)pdm09
viruses showed highly reduced inhibition with oseltamivir, one A(H1N1)pdm09 virus showed highly
reduced inhibition with zanamivir and three B/Victoria viruses showed highly reduced inhibition
with zanamivir.

Keywords: influenza, vaccines, GISRS, surveillance, laboratory, annual report, WHO

Introduction                                                                 recommendations on which influenza strains
                                                                             should be included in the influenza vaccine for
The World Health Organization (WHO)                                          the upcoming influenza season in either the
Collaborating Centre for Reference and Research                              northern or southern hemisphere. This report
on Influenza in Melbourne (the Centre) is                                    summarises the results of virological surveil-
part of the World Health Organization Global                                 lance activities undertaken at the Centre in
Influenza Surveillance and Response System                                   Melbourne during 2019.
(WHO GISRS). GISRS is a worldwide network
of laboratories that was established in 1952 to                              Two types of influenza viruses (A and B) cause
monitor changes in influenza viruses circulat-                               significant disease in humans. Influenza A
ing in the human population, with the aim of                                 viruses are further classified into subtypes,
reducing influenza’s impact through the use                                  based on their haemagglutinin (HA) and neu-
of vaccines and antiviral drugs.1,2 The Centre                               raminidase (NA) surface proteins. Globally,
in Melbourne is one of five such Collaborating                               there are currently two influenza A subtypes
Centres (others are in Atlanta, Beijing, London                              circulating in the human population – A(H1N1)
and Tokyo) that monitor antigenic and genetic                                pdm09 and A(H3N2). Influenza B viruses are
changes in circulating human influenza viruses;                              not classified into subtypes; however, there are
the Centre participates in making twice-yearly                               two distinct co-circulating lineages of influenza

health.gov.au/cdi            Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021    1 of 16
B viruses – B/Victoria/2/87 (B/Victoria lineage)                       B/Colorado/06/2017-like (Victoria lineage), and
and B/Yamagata/16/88 (B/Yamagata lineage).                             B/Phuket/3073/2013-like (Yamagata lineage)
Influenza C viruses are also detected each year                        viruses that were recommended for inclusion
from humans, but these viruses do not cause                            in the southern hemisphere 2019 influenza
severe disease and are not a major focus of                            vaccine. In recent years (including 2019), HI
influenza surveillance.                                                assays involving A(H3N2) viruses have been
                                                                       performed in the presence of 20 nM oseltamivir
Methods                                                                carboxylate (OC) to reduce non-specific bind-
                                                                       ing of the NA protein.5 The addition of OC
Virus isolation                                                        reduces the number of influenza virus isolates
                                                                       that can be tested by HI because around 11% of
All A(H1N1)pdm09 and influenza B viral iso-                            viruses lose the ability to bind RBC and there-
lates received at the Centre were re-passaged in                       fore cannot be assayed by HI. To test a subset
cell culture using Madin-Darby Canine Kidney                           of these viruses, the Centre has employed the
(MDCK) cells, whilst all A(H3N2) viral isolates                        Focus Reduction Assay (FRA), a microneutrali-
were re-passaged in MDCK-SIAT-1 cells.3 Virus                          sation assay which is more specific and sensitive
isolation in cell culture was also attempted                           than the HI assay and does not require bind-
from a selection of original clinical specimens                        ing to RBCs.6 The FRA utilised the same ferret
received using the same cell types as described                        antisera as did the HI assay and was performed
above when the type/subtype was known. A                               as previously described,7 but with 1.2% Avicell
smaller subset of influenza-positive original                          RC591 (IMCD Mulgrave, Australia) replacing
clinical samples was directly inoculated into                          the carboxymethyl cellulose.
eggs and a qualified cell line to generate poten-
tial candidate vaccine viruses (CVV).                                  Genetic analysis

Antigenic analysis                                                     For influenza-positive samples that failed to
                                                                       grow in MDCK cells, real-time reverse tran-
The antigenic properties of influenza viral iso-                       scription polymerase chain reaction (RT-PCR)
lates were analysed using the haemagglutination                        was performed to determine the influenza type/
inhibition (HI) assay as previously described4                         subtype/lineage using the CDC Influenza Virus
and by the Focus Reduction Assay (FRA) for a                           Real-Time RT-PCR kit.i
subset of A(H3N2) viruses. The majority of the
HI assays were performed using the TECAN                               A substantial subset of influenza viruses ana-
Freedom EVO200 robot platform which incor-                             lysed at the Centre underwent genetic analysis
porates a camera (SciRobotics, Kfar Saba,                              by sequencing of viral RNA genes – usually
Israel) and imaging software (FluHemaTM) for                           HA and NA genes as well as the matrix gene
automated analysis. In HI assays, viruses were                         for influenza A viruses and non-structural pro-
tested for their ability to agglutinate turkey                         tein gene (NS) for influenza B viruses. Whole
(A(H1N1)pdm09 and B viruses) or guinea pig                             genome sequencing (WGS) of a smaller subset
(A(H3N2)) red blood cells (RBC) in the pres-                           of viruses was also performed.
ence of post-infection ferret antisera raised
against several reference viruses. Isolates were
identified as antigenically similar to the refer-                      i    The CDC Influenza Virus Real-Time RT-PCR Influenza A/B
ence strain if the test samples had a titre that                            Typing Panel (RUO) (Catalog No. FluRUO-01), FR-198, was
was no more than 4-fold higher than the titre                               obtained through the International Reagent Resource,
of the homologous reference strain. During                                  Influenza Division, WHO Collaborating Center for Surveillance,
2019, results were reported with reference                                  Epidemiology and Control of Influenza, Centers for Disease
to the A/Michigan/45/2009 (H1N1pdm09)-                                      Control and Prevention, Atlanta, GA, USA. https://www.
like, A/Switzerland/8060/2017 (H3N2)-like,                                  internationalreagentresource.org/.

2 of 16              Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021              health.gov.au/cdi
For sequencing, RNA was extracted from iso-                            Australia). For reporting purposes, ‘highly
lates or original clinical specimens using either                      reduced inhibition’ of influenza A viruses has
a manual QIAGEN QIAamp Viral RNA kit                                   been defined by WHO as a ≥ 100-fold increase
or the automated QIAGEN QIAXtractor plat-                              in IC50 in a NAI assay. For influenza B viruses,
form, followed by RT-PCR using the BIOLINE                             this figure was a ≥ 50-fold increase. However, it
MyTaq one step RT-PCR kit according to the                             should be noted that the relationship between
manufacturer’s recommendations, with gene-                             the IC50 value and the clinical effectiveness
specific primers (primer sequences available on                        of a neuraminidase inhibitor is not yet well
request). Conventional Sanger sequencing was                           understood and a small or medium reduction
carried out on PCR products using an Applied                           in inhibition may not be clinically significant.
Biosystems 3500XL Genetic Analyzer (Applied
Biosystems, Foster City, CA, USA). Sequence                            Viruses found to have highly reduced inhibition
assembly was performed using the Geneious                              by either oseltamivir or zanamivir underwent
Prime software version 9.0.4 (Biomatters Ltd,                          genetic analysis using pyrosequencing, Sanger
Auckland, New Zealand).                                                sequencing or WGS to determine the presence
                                                                       of amino acid substitutions in the NA protein
WGS was performed on a selection of viruses                            that were associated with the reduction of inhi-
using the SuperScript-III One-Step Platinum                            bition by neuraminidase inhibitors. For exam-
Hi-Fi PCR kit according to the manufacturer’s                          ple, a change from histidine to tyrosine at posi-
recommendations, with universal primers                                tion 275 (H275Y) of the NA protein of A(H1N1)
(primer sequences available on request). WGS                           pdm09 viruses is known to reduce inhibition by
was conducted using an Applied Biosystems                              oseltamivir, as does the H273Y NA mutation in
Ion TorrentTM Personal Genome MachineTM                                B viruses.9 Pyrosequencing was also performed
(PGM) System according to the manufacturer’s                           on original clinical specimens of selected
recommendations. These sequences were ana-                             viruses which may have contained a known
lysed using a proprietary pipeline, FluLINE.8                          mutation such as H275Y if no isolate was avail-
Phylogenetic analysis was performed using                              able for phenotypic testing. Pyrosequencing
Geneious 9.0.4 and FigTree v1.3.1 software.                            was performed as previously described10 using
                                                                       the MyTaq One-Step RT-PCR Kit (QIAGEN,
Antiviral drug resistance testing                                      Hilden, Germany) for virus amplification, with
                                                                       pyrosequencing reactions performed using
Circulating viruses were tested for their                              the PyroMark instrument (QIAGEN, Hilden,
sensitivity to the currently-used neurami-                             Germany).
nidase inhibitors oseltamivir (Tamiflu) and
zanamivir (Relenza). The neuraminidase                                 Candidate vaccine strains
inhibition (NAI) assay used was a func-
tional fluorescence-based assay using the                              The viruses used in production of human influ-
substrate     2’-(4-methylumbelliferyl)-α-D-N-                         enza vaccines are required by regulatory author-
acetylneuraminic acid (MUNANA), in which                               ities to be isolated and passaged in embryonated
the susceptibility of test viruses to the antiviral                    hen’s eggs or qualified cell lines11–13 directly from
drugs was measured in terms of the drug con-                           human clinical respiratory samples. The Centre
centration needed to reduce the influenza neu-                         has undertaken primary isolation of selected
raminidase enzymatic activity by 50% (IC50),                           viruses from clinical samples directly into eggs,
and compared to values obtained with sensitive                         using previously described methods.14 Briefly,
reference viruses of the same subtype or line-                         the viruses were inoculated into the amniotic
age. NAI assays were performed as previously                           cavity of embryonated eggs and, once virus
described,9 with the incorporation of a robotic                        growth was established, isolates were passaged
platform by Tecan EVO 200 and Infinite 200Pro                          in the allantoic cavity until a sufficient titre was
for liquid handling and plate reading (Tecan                           obtained. Egg incubation conditions differed

health.gov.au/cdi      Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021        3 of 16
slightly, with A(H1N1)pdm09 and A(H3N2)                                A(H1N1)pdm09 and B. For samples received
viruses incubated at 35 oC for three days, and                         from Australia where the lineage was con-
influenza B viruses incubated at 33 oC for three                       firmed, B/Victoria viruses predominated sig-
days. In addition, selected clinical samples were                      nificantly over B/Yamagata viruses (93% and
inoculated into the qualified cell line MDCK                           7% of B viruses respectively). Overall, isolation
33016PF (Seqirus Limited, Holly Springs, NC,                           and re-passaging was attempted for 9,146 (99%)
USA)15 and incubated at 35 oC for three days,                          of the samples received and this yielded 6,101
with viral growth monitored by haemagglu-                              isolates (overall isolation rate of 67%). Isolation
tination of turkey or guinea pig RBC. These                            rates were lower for clinical specimens (60.5%)
isolates were then analysed by HI assay, real                          than for virus isolates received (94.9%). Of the
time RT-PCR and genetic sequencing using the                           viruses for which type and subtype could be
methods described above.                                               confirmed, isolation rates by cell propagation
                                                                       were 75% (1,767/2,350) for A(H1N1)pdm09;
Results                                                                81% (3,150/3,911) for A(H3N2); and 81%
                                                                       (1,142/1,407) for influenza B. However, amongst
During 2019, the Centre received 9,266 samples                         these viruses, 15% (464/3,150) of A(H3N2) iso-
(including 7,687 clinical specimens, 1,014 virus                       lates did not reach sufficient titres for antigenic
isolates and 569 paired specimens and isolates)                        analysis. A total of 4,445 viral isolates were
from 40 laboratories in 17 countries (Figure                           successfully characterised by HI assay, and
1). As in previous years, most samples were                            were compared to the 2019 reference viruses
submitted by laboratories in the Asia-Pacific                          (Table 1). In addition, 991 samples were charac-
region,16–19 with the majority received from                           terised by real-time RT-PCR to determine their
Australia (7,410 samples; 80%). However, unlike                        type/subtype or lineage. Sanger sequencing and
previous years, a large number of samples were                         WGS techniques were used to sequence the HA
received between January and April, which is                           genes of 2,487 viruses. The full genomes of 415
before the typical Southern Hemisphere tem-                            viruses were also sequenced using either Sanger
perate regions influenza season. Figure 2 shows                        sequencing or WGS. Of the samples for which
the weekly temporal distribution of samples                            results could be obtained by antigenic or genetic
sent to the Centre by type and subtype/line-                           analysis (n = 6,368), influenza A(H3N2) viruses
age. During 2019, influenza A(H3N2) was the                            predominated, comprising 49% (n = 3,133) of
predominant circulating strain, followed by                            viruses received and analysed.
Figure 1: Geographic spread of influenza laboratories sending viruses to the Centre during 2019

4 of 16              Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021   health.gov.au/cdi
Table 1: Antigenic analysis of viruses received by the Centre in 2019, by geographic region of origin

                                                                                                                     A(H1N1)pdm09 reference strain:                     A(H3N2)a reference strain:                    B/Victoria reference strain:                  B/Yamagata reference strain:

health.gov.au/cdi
                                                                                                                         A/Michigan/45/2015 (cell)                   A/Switzerland/8060/2017 (cell)                    B/Colorado/06/2017 (cell)                      B/Phuket/3073/2013 (cell)

                                                                                                                                             Low reactor                                    Low reactor                                    Low reactor                                   Low reactor
                                                                                                Region                    Like                                           Like                                           Like                                           Like
                                                                                                                                                (%)                                            (%)                                            (%)                                           (%)

                                                                                                Australasia               1,136                 31 (2.7%)                1,214                347 (22.2%)                503                  64 (11.3%)                 41                1 (2.4%)

                                                                                                South East Asia            298                   26 (8%)                  58                  96 (62.3%)                 118                  48 (28.9%)                 79                   0

                                                                                                Pacific                    80                  34 (29.8%)                 25                   5 (16.7%)                 99                   22 (18.2%)                 2                    0

                                                                                                Africa                      3                      0                       4                   11 (73.3%)                 0                       0                      0                    0

                                                                                                South Asia                 13                      0                       0                   5 (100%)                   18                      0                      4                    0

                                                                                                East Asia                  31                   3 (8.8%)                   4                    1 (20%)                   11                   9 (45%)                   1                    0

                                                                                                Total                    1,561                94 (5.7%)                 1,305               465 (26.3%)                 749                 143 (16%)                   127               1 (0.8%)

                                                                                            a    Note that a small number of A(H3N2) virus isolates that were obtained could not be analysed by HI assay due to low haemagglutination assay (HA) titre in the presence of oseltamivir.

Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021
5 of 16
Figure 2: Number of samples received at the Centre by week of sample collection 2019
                              300

                                                                                                                                                      A(H1N1)pdm09
                                                                                                                                                      A(H3N2)
                              250
                                                                                                                                                      B/Victoria
                                                                                                                                                      B/Yamagata

                              200
 Number of samples received

                              150

                              100

                              50

                               0
                                    1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51

                                                                                    Week of sample collection

A(H1N1)pdm09                                                                                              Of 1,701 A(H1N1)pdm09 viruses tested, three
                                                                                                          viruses exhibited highly reduced inhibition
Of the 1,655 A(H1N1)pdm09 isolates analysed                                                               by oseltamivir and one virus exhibited highly
by HI assay using ferret antisera in 2019, a                                                              reduced inhibition by zanamivir. The viruses
majority (94%) were antigenically similar to the                                                          showing highly reduced inhibition by oseltami-
vaccine reference strain A/Michigan/45/2015                                                               vir (two from Australia and one from Malaysia)
(Table 1).                                                                                                were confirmed to contain the H275Y substitu-
                                                                                                          tion in their NA genes, a known mutation that
Sequencing and phylogenetic analysis of HA                                                                is associated with highly reduced inhibition by
genes from 644 viruses showed that all A(H1N1)                                                            oseltamivir. Another NA substitution linked
pdm09 viruses sent to the Centre during 2019                                                              to the reduction in inhibition by zanamivir
fell into the 6B.1 clade (Figure 3). The majority                                                         was also identified in one of the viruses from
of these viruses reacted in a similar manner to                                                           Australia.20 This virus was confirmed to contain
the 2019 vaccine virus A/Michigan/45/2015 in                                                              the E119G substitution in its NA gene.
HI assays using ferret antisera.

Eighteen A(H1N1)pdm09 viruses were inocu-
lated into eggs for isolation of candidate vaccine
strains with 16 (89%) successfully isolated; all
fell into the genetic subclade 6B.1A. Thirty-nine
viruses were inoculated into the qualified cell
line MDCK 33016PF, of which 25 (64%) grew
successfully and all also fell into the genetic
subclade 6B.1A.

6 of 16                                                 Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021                     health.gov.au/cdi
Figure 3: Phylogenetic tree of haemagglutinin genes of A(H1N1)pdm09 viruses received by the
Centre during 2019
                                                                                                         A/Victoria/265/2019 oct
                                                                                                    A/Ratchaburi/435/2019 nov
                                                                                                    A/Lopburi/4448/2019 dec
  Legend                                                                                               A/Perth/182/2019 dec
                                                                                                 niidA/Okinawa/93/2019 aug
                                                                                                             A/Perth/1156/2019 dec
  #2019 SOUTHERN HEMISPHERE VACCINE STRAIN                                                                       A/South Australia/476/2019 dec
                                                                                                   A/Sydney/1237/2019 nov
                                                                                                      A/Brisbane/146/2019 oct
  e: egg isolate                                                                                         A/Canberra/411/2019 nov
                                                                                                         A/Perth/1154/2019 oct
                                                                                                      A/Victoria/2569/2019 nov
  ^REFERENCE VIRUS                                                                                     A/Philippines/39/2019 oct
                                                                                                         A/Chanthaburi/443/2019 nov
                                                                                                         A/Malaysia/RP2260/2019 oct
  │Braces indicate clades                                                           R45K
                                                                                                               A/Philippines/34/2019 oct
                                                                                    T120I
                                                                                                         A/Sydney/454/2019 oct
  (+/-) Indicates gain/loss of a potential glycosylation site.                                           A/Brisbane/149/2019 oct
                                                                                                       A/Brisbane/144/2019 oct
                                                                                                    A/Philippines/37/2019 oct
  Scale bar represents 0.3% nucleotide sequence difference                                          A/Canberra/415/2019 nov
                                                                                                         A/South Australia/1128/2019 dec
  between viruses. Amino acid changes relative to the outgroup                        D187A                A/Perth/178/2019 nov
  sequence (A/CALIFORNIA/07/2009e) are shown.                                         Q189E A/Brisbane/142/2019 oct
                                                                                                       A/Malaysia/UM015/2019 oct
                                                                                                 A/Sydney/1235/2019 nov
                                                                               D187V           A/Guangdong-Maonan/SWL1536/2019e jun
                                                                                               A/Victoria/2455/2019e aug
                                                                                                       A/Victoria/2454/2019e aug
                                                                                                    A/Malaysia/RP2253/2019 oct
                                                                                                       A/Lopburi/440/2019 nov
                                                                                                                A/Sydney/451/2019 oct
                                                                                                          A/Malaysia/RP2255/2019 oct                       183P-5A
                                                                                                          A/Chiang Rai/1391/2019 dec
                                                                                              A186T A/Victoria/267/2019 oct
                                                                                                                A/Darwin/739/2019 oct
                                                                                                A/Malaysia/RP2261/2019 oct
                                                                                                                  A/Nakhonphanom/487/2019 dec
                                                                                                             A/Bangkok/426/2019 oct
                                                                                                         A/Nakhonsithammarat/425/2019 oct
                                                                                                           A/South Australia/466/2019 nov
                                                                                             A/South Africa/R05624/2019 may
                                                                                                       A/South Australia/451/2019 oct
                                                                                                  A/Victoria/2568/2019 nov                                           6B.1A/183P-5
                                                                                                     A/Cambodia/D1216368/2019 nov
                                                                                                              mohA/Singapore/GP2220/2019 nov
                                                                                                                A/Victoria/2570/2019 nov
                                                                             K504R                   A/Philippines/31/2019 oct
                                                                                                       A/Sri Lanka/15/2019 apr
                                                                                                A/Darwin/764/2019 nov
                                                                                                  A/Brunei/8/2019 mar
                                                                                           A/Macau/600148/2019 jan
                                                                                                       A/Cambodia/d0619361/2019 may
                                                                                                A/New Caledonia/87/2019 may
                                                                                                              A/South Australia/477/2019 dec
                                                                                             A/Timor Leste/41/2019 apr
                                                                                                     A/New Caledonia/67/2019 jun
                                                                                             A/New Caledonia/95/2019 jun
                                                                                                         A/Sri Lanka/40/2019 aug
                                                                                                       A/Victoria/214/2019e aug
                                                                            N129D                 A/Darwin/639/2019e aug
                                                                             T185I                   A/Victoria/255/2019 sep
                                                                                             A/Victoria/212/2019e aug
                                                                                           ^A/DARWIN/6/2018e
                                                                                           A/Darwin/123/2018e
                                                                                             A/Darwin/122/2018e
                                                                                                A/Darwin/125/2018e
                                                                                                A/Darwin/1024/2019 nov
                                                                                             A/Perth/193/2019 nov
                                                                                                A/Canberra/417/2019 nov
                                                                                   K520A
                                                                    N260D                         A/Darwin/738/2019 oct
                                                                                                                        A/CANBERRA/337/2019e aug
                                                                                                                       A/Canberra/394/2019 oct
                                                                                                                     A/Canberra/400/2019 oct
                                                                                                                 A/South Australia/456/2019 oct
                                                                                                                       A/Darwin/784/2019 dec
                                                                                        K130N, K160M                   A/South Australia/471/2019 nov   183P-5B
                                                                                        T216K, H296M         A/Philippines/27/2019  sep
                                                                                                             A/Wellington/36/2019 jun
                                                                                                               A/Brisbane/147/2019 oct
                                                                                                            A/Iowa/12/2019e jun
                                                                                         ^crickA/SWITZERLAND/3330/2017e
                                                            E235D                      A/Fiji/54/2018e
                                                            V520A                               A/South Australia/49/2018e sep
                                                                                          A/Darwin/4/2018e oct
                                                                                                  A/Brisbane/59/2018e
                                                                              P183S      ^A/SOUTH AUSTRALIA/272/2017e
                                                                         T120A                         A/Fujian Gulou/SWL1884/2018e 183P-6
                                                                                                      A/Newcastle/31/2019 mar
                                                                                                  A/South Africa/R03973/2019 apr
                                                                                              ^A/BRISBANE/157/2018
                                                                                                A/Canberra/13/2019e jan
                                                                                                  A/Darwin/102/2019e mar
                                                                                                  A/Newcastle/46/2019e mar
                                                                                                        A/Brunei/5/2019e feb
                                                                                                        A/Brunei/54/2019 apr
                                                                                               A/Fiji/26/2019 mar
                                                                                               A/Fiji/51/2019 mar                       183P-2
                                                                      L233I                A/Brisbane/70/2018e
                                                                      V520A                 A/Brisbane/72/2018e
                                                                                A/Brisbane/68/2018e                                                        6B.1A
                                                                                ^A/CHRISTCHURCH/506/2018e
                                                                                                  A/Cambodia/FSS40727/2019 jun
                                                        R45G, P282A             ^A/TOWNSVILLE/21/2018
                                                        I298V
                                                                                  A/Christchurch/515/2018e
                                                                                                 ^A/PERTH/183/2018 nov                   183P-4
                                                                                      ^A/BRISBANE/02/2018e
                                                                                                  A/Newcastle/45/2018e
                                                                                        A/BeijingXicheng/SWL1633/2018e
                                                                                                                                 183P-1
                                                                                                               A/Timor-Leste/94/2019 apr
                                                                          K302T, I404M                       A/Timor Leste/34/2019 mar
                                         S74R, S164T, S183P              N496S, E506D                       A/Victoria/700/2019 mar         183P-7
        P83S, S84N, D97N, S162N (+)      R223Q, I295V                                                          ^A/INDIANA/30/2019
         K163Q, S185T, S203T, I216T                                                                       A/Macau/600080/2019 jan
         A256T, K283E, I321V, E374K                                           ^cdcA/MEXICO/2549/2018 183P-3
                      S451N, E499K      A/MICHIGAN/45/2015e ^A/BRISBANE/37/2017
                                    ^A/CALIFORNIA/07/2009e

                                                          0.003

health.gov.au/cdi                            Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021                                        7 of 16
A(H3N2)                                                                 None of the 2,323 A(H3N2) viruses tested by
                                                                        NAI assay showed highly reduced inhibition by
Antigenic analysis of 2,104 A(H3N2) subtype                             oseltamivir or zanamivir.
isolates using the HI assay showed that 26%
were low reactors to the ferret antisera prepared                       Influenza B
against the cell-propagated reference strain A/
Switzerland/8060/2017/2017 (Table 1). However,                          Amongst influenza B viruses received at the
99% of viruses were low reactors to the ferret                          Centre during 2019, B/Victoria-lineage viruses
antisera prepared against the egg-propagated                            were predominant over B/Yamagata-lineage
strain A/Switzerland/8060/2017 (data not                                viruses (Figure 2). A total of 1,020 influenza B
shown). An additional 464 A(H3N2) viruses                               viruses were characterised by HI assay. Almost
were inoculated and isolated by cell culture                            all B/Yamagata-lineage viruses were antigeni-
but did not reach sufficient titres for antigenic                       cally similar to the B/Phuket/3073/2013-like
analysis, whilst a further 334 were successfully                        vaccine virus, while 84% of B/Victoria-lineage
isolated but did not reach sufficient titres when                       viruses were antigenically similar to the
tested by HI assay in the presence of oseltamivir                       B/Colorado/06/2017 vaccine virus (Table 1).
carboxylate.
                                                                        Sequencing was performed on HA genes from 367
A total of 75 A(H3N2) viruses that could not be                         B/Victoria viruses and 88 B/Yamagata viruses. A
characterised by HI assay were analysed using the                       small number of B viruses (51/367; 14%) were
FRA assay. The FRA assay indicated that 16% of                          genetically similar to the B/Colorado/06/2017
these viruses showed greater than four-fold dif-                        reference virus, with a two-amino-acid deletion
ference in titre compared to the cell-propagated                        in the HA protein (positions 162–163) (Figure 5);
reference strain A/Switzerland/8060/2017; how-                          however, the majority of viruses (272/367; 74%)
ever, the majority of viruses (93%) had a greater                       had a three-amino-acid deletion in the HA pro-
than four-fold difference in titre compared to                          tein at positions 162–164 and formed a separate
the egg-propagated strain (data not shown).                             phylogenetic clade from the B/Colorado/06/2017
                                                                        clade. All B/Yamagata-lineage viruses belonged
The HA genes of 1,309 A(H3N2) viruses                                   to genetic clade 3 (or Y3), which is the same
were sequenced. Phylogenetic analysis indi-                             genetic clade as the 2019 vaccine virus B/
cated that the majority of circulating viruses                          Phuket/3073/2013 (Figure 6).
fell into subclade 3C.2a1b based on their
HA genes, whereas the 2019 vaccine strain,                              Egg isolation was attempted for 15 B/Victoria
A/Switzerland/8060/2017 fell into subclade                              and eight B/Yamagata-lineage viruses, result-
3C.2a2 (Figure 4). A small number of A(H3N2)                            ing in the successful isolation of 11 (73%)
viruses fell into the 3C.3a and 3C.2a3 clades.                          B/Victoria-lineage viruses and four (50%) B/
                                                                        Yamagata-lineage viruses. All B/Victoria-lineage
Forty-seven viruses were inoculated into                                viruses isolated were from genetic subclade V1A,
eggs, of which 27 (57%) grew successfully and                           two of which were further grouped into V1A.1
consisted of 21 viruses from genetic subclades                          and eight others in V1A.3. All B/Yamagata-
3C.2a1b+131K and two from 3C.2a1b+135K.                                 lineage viruses isolated were from genetic clade
Additionally, four subclade 3C.3a viruses were                          Y3. For viruses inoculated into the qualified
isolated. Fifty-seven viruses were inoculated into                      cell line MDCK 33016PF, nine of 16 (56%) B/
the qualified cell line MDCK 33016PF, of which                          Victoria-lineage viruses and four (80%) of five B/
38 (67%) grew successfully, with 23 viruses from                        Yamagata-lineage viruses were isolated. At least
genetic subclades 3C.2a1b+131K, four from                               one representative from the major clades of each
3C.2a1b+135K and 11 from 3C.3a.                                         B lineage was isolated. A total of 21 viruses were
                                                                        inoculated into the qualified cell line MDCK
                                                                        33016PF, of which 13 (62%) grew successfully.

8 of 16               Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021   health.gov.au/cdi
Figure 4: Phylogenetic tree of haemagglutinin genes of A(H3N2) viruses received by the Centre
during 2019
           Legend                                                                                                                 A/South Australia/464/2019 nov
                                                                                                                       A/South Australia/457/2019 oct
           #2019 SOUTHERN HEMISPHERE VACCINE STRAIN                                                                      A/Victoria/2542/2019 oct
                                                                                                                       A/South Australia/467/2019 nov
                                                                                                                       A/Victoria/2854/2019 oct
           e: egg isolate                                                                                           A/Victoria/2540/2019 oct
                                                                                                                         A/Victoria/2490/2019 sep
                                                                                                                  A/South Australia/468/2019 nov
           ^REFERENCE VIRUS                                                                                                 A/Shanghai-Jiading/197/2019 dec
                                                                                                                       A/Victoria/2580/2019 nov
           │Braces indicate clades                                                                                    A/Sydney/1228/2019 sep
                                                                                                                           A/Tasmania/1038/2019 oct              +197R
                                                                                                                       A/Victoria/2565/2019 oct
           (+/-) Indicates gain/loss of a potential glycosylation site.                         Q197R             A/Perth/1051/2019 jun
                                                                                                E484G             A/Victoria/2479/2019 sep
                                                                                                                      A/Darwin/727/2019 oct
           Scale bar represents 0.3% nucleotide sequence difference                                                 A/South Australia/439/2019 oct
           between viruses. Amino acid changes relative to the outgroup                                            A/Victoria/169/2019e jul
           sequence (A/TEXAS/50/2012) are shown.                                                              A/Tasmania/1037/2019 sep
                                                                                                                  A/Tasmania/557/2019 may
                                                                                                                A/South Australia/447/2019 oct
                                                                                                             A/Canberra/398/2019 oct
                                                                                                           A/Tasmania/1025/2019 jul
                                                                                                                                  A/Sydney/478/2019 sep
                                                                                                                          A/Canberra/412/2019 nov
                                                                                                                  A/Darwin/402/2019e may
                                                                                                              A/Darwin/384/2019e may
                                                                                                               A/Victoria/718/2019e may
                                                                                                             A/South Australia/36/2019e feb
                                                                                                                          A/Nonthaburi/424/2019 oct
                                                                                                               A/Ayutthaya/458/2019 nov
                                                                                                         A/South Africa/R05117/2019 may
                                                                                                               A/New Caledonia/59/2019e mar
                                                                                                               A/Christchurch/516/2019e apr
                                                                                                                     A/New Caledonia/99/2019 jul
                                                                                                                  A/Victoria/2539/2019 oct
                                                                                                             A/Brisbane/1137/2019 sep
                                                                                                           A/Christchurch/514/2019e apr                                  3C.2a1b+131K
                                                                                                           A/Sri Lanka/41/2019 aug
                                                                                                           A/Victoria/2534/2019 sep
                                                                                                          A/South Africa//R06415/2019 jun
                                                                                                           A/Sri Lanka/35/2019 jul
                                                                                                            A/Cambodia/FSS40728/2019 jun
                                                                                                              A/South Australia/82/2019e feb
                                                                                                         A/Newcastle/42/2019e mar
                                                                                                       ^A/SOUTH AUSTRALIA/34/2019e feb
                                                                                                         ^A/NEWCASTLE/82/2018e
                                                                                                            A/Sydney/53/2019e mar
                                                                                      V347M         A/Hawkes Bay/1/2019 mar
                                                                                                 V505I        A/Bangkok/454/2019 nov
                                                                                                               A/Victoria/2573/2019 nov
                                                                                                            A/South Australia/39/2019e feb
                                                                                                  A/Newcastle/83/2018e
                                                                                                                                       A/ChiangRai/449/2019 nov
                                                                                   T131K                               A/South Australia/469/2019 nov
                                                                                   V529I                             A/Canberra/407/2019 oct
                                                                                                                             A/Victoria/2566/2019 nov
                                                                                                                       A/South Australia/474/2019 nov
                                                                                                                                A/Malaysia/RP2256/2019 oct
                                                                                                                               A/Sydney/1234/2019 oct
                                                                                                                          crickA/Qatar/16-VI-19-0049409/2019 aug
                                                                                             K83E                         A/Victoria/2845/2019 oct
                                                                                                                             A/Sri Lanka/23/2019 jul
                                                                                                             A/Sri Lanka/27/2019 jul
                                                                                                                      mohA/Singapore/EN0894/2019 nov
                                                                                                                         A/Victoria/213/2019 aug
                                                                                                                         A/Philippines/46/2019 sep
                                                        E62G, K92R, N121K, R142G                                         A/Victoria/268/2019 oct
                                                        K160T(+), N171K, H311Q                                        A/Victoria/2833/2019 sep
                                                        I406V, G484E                                                  A/Darwin/730/2019 oct
                                                                                                              E50K A/Philippines/40/2019 oct
                                                                                                                              A/Philippines/51/2019 nov
                                                                                                                                                               +137F
                                                                                                                        cdcA/Hong Kong/2671/2019 jun
                                                                                                                 A/Macau/603415/2019may
                                                                                                  S137F               A/Hong Kong/45/2019
                                                                                                                      mohA/Singapore/TT0882/2019 nov
                                                                                                                                A/South Australia/2/2019e jan
                                                                                                                                                                      3C.2a1b+135K
                                                                                                                              A/South Australia/4/2019e jan
                                                                                                                            A/Brisbane/148/2019e oct
                                                                                                                              A/Victoria/2574/2019 nov
                                                                                                            A/Hong Kong/681/2018e
                                                                                                               A/Timor Leste/5/2019 mar
                                                                                                            A/South Africa/R03989/2019 apr
                                                                                                        ^A/FIJI/71/2017
                                                                               T135K(-) G62E                        ^A/SYDNEY/22/2018e
                                                                                         K135N         ^A/PHILIPPINES/13/2017                  3C.2a1b+135N
                                                         T131K, R142K, L194P, R261Q           A/SWITZERLAND/8060/2017e
                                                                                          A/South Australia/10/2018e
                                                                                                                             3C.2a2
                                                                                          A/Timor Leste/3/2019 mar
                                                            T30A, T128A(-), T135K(-)            A/TimorLeste/43/2019 mar
                                L3I, N144S(-)       S144K   R142G, R261Q
                                                                                                   A/Malaysia/RP0118/2019    3C.2a3
                                S159Y, V186G                                ^A/SINGAPORE/TT1374/2016e
                                Q311H, D489N
                                                      ^A/MICHIGAN/15/2014
                                                     ^A/HONG KONG/4801/2014e 3C.2a

                                                                                                      A/Townsville/60/2019 oct
                                                                                                           A/Brisbane/141/2019 oct
                                                                                                        A/Darwin/725/2019 oct
                                                                                                      A/Brisbane/145/2019 oct
                                                                                                   A/Brisbane/1024/2019 jul
                                                                                                   A/Darwin/721/2019 sep
                                                                                                   A/Townsville/59/2019 oct
                                                                                                 A/Sydney/475/2019 sep
                                                                                                        A/Victoria/2482/2019 sep
                                                                                   K82R           A/South Australia/458/2019 oct
                                                                                                    A/Wellington/53/2019 sep
                                                                       H56Y, N121D          A/Canberra/23/2019 feb
                                                                                              A/Perth/1113/2019 jul                        3C.3a
                                                                                            A/South Australia/218/2019e mar
                                                                                ^A/KANSAS/14/2017e
                                                                    I478M                             A/Victoria/703/2019e apr
                                                                                            A/Newcastle/623/2019e feb
                                                                                                        A/South Australia/470/2019 nov
                                               L3I, S91N, N144K(-)                                        A/South Africa/R06423/2019 jun
                                               V186G, F193S, D489N                        A/South Africa/R06864/2019 jun
                               T128A,(-) A138S                                    A/Beijing/2019 15554/2018e
                               R142G, K326R
                                                                               A/Brisbane/34/2018e
                                                    ^A/SWITZERLAND/9715293/2013e
                               ^A/TEXAS/50/2012e

                                                                     0.003

health.gov.au/cdi                          Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021                                                    9 of 16
Figure 5: Phylogenetic tree of haemagglutinin genes of B/Victoria-lineage viruses received by the
Centre during 2019

  Legend                                                                                                 N197K(-)
                                                                                                                      B/South Australia/1022/2019 sep
                                                                                                                  B/South Australia/125/2019 oct***
  #2019 SOUTHERN HEMISPHERE VACCINE STRAIN                                                             B/Chiang Rai/431/2019 oct*
                                                                                                             B/Cambodia/FSS42434/2019 nov
                                                                                                         B/Chiang Rai/1387/2019 dec*
  e: egg isolate                                                                                         B/Yasothon/381/2019 aug
                                                                                        E128K                  B/Cambodia/D1225364/2019 dec
  ^REFERENCE VIRUS                                                                                              B/Brunei/17/2019 sep
                                                                                                                B/Victoria/2546/2019 nov
                                                                                                         B/Canberra/84/2019 oct            V1A.3 +128K
  │Braces indicate clades                                                                                  B/Darwin/189/2019 dec
                                                                                                           B/Philippines/31/2019 oct
                                                                                                       B/Darwin/151/2019 oct*
  Scale bar represents 0.3% nucleotide sequence difference                                                      B/Chiang Rai/452/2019 nov
  between viruses. Amino acid changes relative to the outgroup                                               B/Newcastle/1000/2019 jul
  sequence (B/BRISBANE/60/2008e) are shown.                                                                     B/Malaysia/RP2142/2019 oct
                                                                                                         B/Cambodia/FSS41540/2019 dec*
                                                                                                           B/Darwin/161/2019 oct
  (+/-) Indicates gain/loss of a potential glycosylation site.                                           B/Brunei/13/2019 aug
                                                                                                       B/Sri Lanka/29/2019 dec*
                                                                                                    B/Nakhonphanom/412/2019 nov
  2 DEL and 3 DEL indicate subclades containing 2 or 3 amino                                                 B/Cambodia/D1216371/2019 nov
  acid deletions at the positions162/163 and 162-164 respectively.                                       B/Victoria/46/2019 sep
  Deletions are also noted in:                                                                      B/TimorLeste/3/2019     mar
                                                                                                             B/Malaysia/UM008/2019 aug
  * = N197X                                                                                         B/Cambodia/D1216360/2019 nov
  ** = N199X                                                                                             B/Perth/33/2019 jun
  *** =N197X & N199X                                                                                   B/Nakhonphanom/460/2019 nov
                                                                                                           B/Trang/437/2019 nov
                                                                                                    ^B/WASHINGTON/02/2019 jan
                                                                                                           B/Cambodia/D1016373/2019 oct
                                                                                                         B/Macau/602915/2019 apr
                                                                                                       B/Victoria/6/2019 jun
                                                                                                       B/Ratchaburi/415/2019 oct
                                                                                       A202T               B/Victoria/2071/2019 sep
                                                                                                       B/Ayutthaya/362/2019 aug
                                                                                                       B/Philippines/4/2019 jan
                                                                                                             B/Victoria/48/2019 oct**
                                                                                                           B/Sydney/52/2019 nov
                                                                                                        B/Wellington/15/2019 may
                                                                                                      B/Sydney/507/2019 aug                              V1A.3
                                                                                       T199A(-)         B/Darwin/20/2019e mar                            3 DEL
                                                                                                       B/Darwin/7/2019e mar**
                                                                                                      B/Darwin/8/2019e mar**
                                                                                                        B/Malaysia/RP2138/2019 jul
                                                                                                      B/Townsville/8/2019 sep                                      V1A
                                                                                                       B/South Australia/40/2019 apr
                                                                                                    B/New Caledonia/10/2019 jul
                                                                                                    B/Vanuatu/2/2019 may
                                                                                           G133R    B/WallisFutuna/7/2019 jul
                                                                                                           B/Victoria/2111/2019 nov
                                                                                                    B/Canberra/76/2019 sep**
                                                                       A127T, N150K                      B/Newcastle/8/2019    aug
                                                                       G184E, N197D                       B/Sri Lanka/26/2019 dec
                                                                       R279K                          B/Canberra/87/2019 oct
                                                                                                B/Brisbane/35/2018e
                                                                               K136E                    B/Victoria/705/2018e
                                                                                                              B/Philippines/28/2019 oct
                                                                                                     B/Philippines/27/2019 oct
                                                                                                       B/Victoria/2113/2019 dec            V1A.3 +150K
                                                                                                         B/Victoria/2110/2019 nov
                                                                                                cdcB/Florida/39/2018
                                                                               I180T, K209N         B/Victoria/905/2019           V1A.2
                                                                                                  ^B/HONG KONG/269/2017e 3 DEL
                                                                                 ^B/BRISBANE/46/2015e
                                                                                                      B/Sydney/1/2019 jan
                                                                                                        B/Fiji/2/2019 apr
                                                                                                      B/Brunei/1/2019 jan
                                                                                                     B/Perth/1031/2019 jun
                                                                                     ^B/TOWNSVILLE/8/2016
                                                                                                          B/TimorLeste/5/2019 feb
                                                                                                      B/Victoria/25/2019 aug
                                                                              I180V
                                                                                                    B/Perth/32/2019    jun
                                                                              R498K
                                                                                       N197S(-)         B/Perth/1035/2019 jun          V1A.1
                                                                                                      B/Darwin/69/2019 jun              2 DEL
                                                            I117V, V146I                                  B/Townsville/13/2019 nov
                                                                                  D129G
                                                                                                      B/Philippines/1/2019 jan
                                                                 K165N                      # B/COLORADO/6/2017e
                                                      N129D      N197S(-)
                                                                                          B/Maryland/15/2016
                                                                 T221I
                                                                                          B/ZhejiangWuxin/113/2018e
                                                                                              cdcB/CHONGQINGBANAN/1840/2017
                                                              ^cdcB/TEXAS/02/2013e**
                                                          ^B/DARWIN/40/2012*
                                                           ^B/SOUTH AUSTRALIA/81/2012e
                                                              ^B/BRISBANE/18/2013e*
                                                                        ^B/VICTORIA/502/2015e
                                                    ^B/BRISBANE/60/2008e
                                               ^B/SYDNEY/508/2010e V1B

                                                                          0.003

10 of 16                            Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021                             health.gov.au/cdi
Figure 6: Phylogenetic tree of haemagglutinin genes of B/Yamagata-lineage viruses received by
the Centre during 2019

                                                                                                                  B/Cambodia/d0503379/2019 apr
                                                                                                                  B/Cambodia/d0528380/2019 may
                                                                                                            B/Mukdahan/17/2019 jan
Legend                                                                                                        B/NakhonSiThammarat/2950/2018
                                                                                                                B/PrachuapKhiriKhan/352/2018
                                                                                                           B/Cambodia/FSS38583/2018
#2019 SOUTHERN HEMISPHERE VACCINE STRAIN                                                                      B/Chanthaburi/349/2018
                                                                                                           B/Sydney/703/2019 mar
                                                                                                            B/Newcastle/1/2019 jan
e: egg isolate                                                                                          B/Cambodia/c1217372/2018
                                                                                                        B/Darwin/1/2019 jan
^REFERENCE VIRUS                                                                                            B/Canberra/2/2019 jan
                                                                                           S120T          nihwB/Finland/164/2019 dec
                                                                                                          B/Brunei/5/2019 feb
│Braces indicate clades                                                                                       B/Victoria/33/2019 aug
                                                                                                               nicrfB/Saint Petersburg/RII 346/2019 dec
                                                                                                                  B/South Australia/6/2019e feb
(+/-) Indicates gain/loss of a potential glycosylation site.                                         V177I      B/South Australia/7/2019 feb
                                                                                                            B/Sydney/44/2018
                                                                                                    D230N B/South Australia/8/2019 feb
Scale bar represents 0.4% nucleotide sequence difference                                  N164K
                                                                                                            B/South Australia/11/2019 feb
between viruses. Amino acid changes relative to the outgroup                                                  B/South Australia/13/2019 feb
sequence (B/FLORIDA/4/2006) are shown.                                                                    crickB/Norway/2992/2019 dec
                                                                                                                  B/Malaysia/RP1205/2019 feb
                                                                                                              B/Malaysia/RP2125/2019 jun
                                                                                           G141R
                                                                                                              B/Darwin/58/2019e may
                                                                                                              B/Brunei/3/2019 jan
                                                                                       D233N(+)                B/Malaysia/RP1248/2019 apr
                                                                                                          B/Philippines/19/2019 jan
                                                                                                         B/Malaysia/RP0882/2019 feb
                                                                                                                    B/Malaysia/RP4022/2018
                                                                                                               B/Brunei/10/2019e mar
                                                                                                        V177I
                                                                                                                  B/Brunei/2/2019 jan
                                                                                                                      B/Malaysia/RP0778/2019 jan
                                                                                                                      B/South Australia/82/2018
                                                                                                                        B/South Australia/86/2018
                                                                                                                  cdcB/Colombia/7437/2019 dec
                                                                                                     B/South Australia/67/2018
                                                                                                         B/Bangkok/332/2018                                Y3
                                                                                                      B/Victoria/15/2018
                                                                                                      B/South Australia/57/2018
                                                                                                                         B/Darwin/25/2018
                                                                                                       N218D             B/Victoria/2042/2018
                                                                                                                       B/Christchurch/500/2018e
                                                                                      D233N(+)           B/Sri Lanka/1/2019 jan
                                                                                                          B/Perth/2/2019 jan
                                                                                                          B/South Australia/53/2018
                                                                                                          B/Sydney/2/2019 jan
                                                                                                          B/Perth/18/2019 apr
                                                                                                              cdcB/Chile/8423/2019 nov
                                                                                                            B/Newcastle/602/2019 jan
                                                                                                                  B/Macau/601172/2019 feb
                                                                                                            B/Philippines/8/2019 jan
                                                                                                              B/South Australia/3/2019 jan
                                                                                                                    B/WallisFutuna/4/2019 may
                                                                                                                    B/Wallis Futuna/2/2019 may
                                                                                                              B/Brisbane/1/2019 jan
                                                                                                              B/Tauranga/1/2018 jun
                                                                                                                      ipB/Bretagne/2404/2019 nov
                                                                                                                afcamB/Nevada/9922/2019 nov
                                                                                                                      B/South Australia/4/2019 jan
                                                                                                                B/Tasmania/503/2019 jul
                                                                                                           B/Cambodia/d0131375/2019 jan
                                                                                                             B/JilinChaoyang/11723/2018e
                                                                                                           B/BeijingChaoyang/12977/2017e
                                                                                                    B/South Australia/34/2018
                                                                                                                  B/Newcastle/56/2018
                                                                                                D230N         B/Victoria/2002/2019 jan
                                                                                                           B/Malaysia/RP0776/2019 jan
                                                                         L173Q
                                                                                                        ^B/PERTH/4/2017
                                                    N116K, D197N(+)      M252V
                                                    K299E, E313K
                                                                                                    ^B/WELLINGTON/40/2017
                                                                                              ^B/CANTERBURY/5/2017
                                                                                                    B/ShanghaiPudongxin/114/2018e
                                                                                    ^B/SYDNEY/10/2016 feb
                                             S150I, N165Y                     #B/PHUKET/3073/2013e
                   K88R, S230G, E479D        N203S, G230D           ^B/WISCONSIN/01/2010e
                                                                      ^cdcB/HUBEIWUJIAGANG/20158/2009e
                                                                     ^B/MASSACHUSETTS/02/2012e Y2
                                      ^B/FLORIDA/4/2006 Y1

                                                                    0.004

health.gov.au/cdi                  Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021                              11 of 16
Of 54 B/Yamagata-lineage viruses tested, none                            The predominant circulating virus in January
displayed highly reduced inhibition by oseltami-                         and February 2019 across Australia was
vir or zanamivir. However, three of the 1,223                            A(H1N1)pdm09, while influenza A(H3N2)
B/Victoria-lineage viruses tested showed highly                          virus submissions began to increase rapidly in
reduced inhibition by zanamivir. Two of the                              March 2019, subsequently becoming the pre-
viruses, one each from Malaysia and Australia,                           dominant circulating strain in 2019. Influenza
contained an E105K substitution in their NA                              A(H3N2) viruses accounted overall for 51%
genes, which has been shown to reduce sus-                               of samples submitted to the Centre, followed
ceptibility to neuraminidase inhibitor drugs.16                          by A(H1N1)pdm09 (30%), while influenza B
A B/Victoria-lineage virus from Malaysia was                             viruses comprised 18% of samples received.
found to contain gene sequence coding for a                              Globally, influenza A viruses were predomi-
novel dual-amino-acid substitution, T146P +                              nant in 2019, with co-circulation of A(H1N1)
N169S, in its NA gene.                                                   pdm09 and A(H3N2). In the southern hemi-
                                                                         sphere, A(H1N1)pdm09 predominated in South
Discussion                                                               America, followed by A(H3N2). By contrast,
                                                                         A(H3N2) predominated in South Africa with
During 2019 the Centre received a larger                                 very few detections of A(H1N1)pdm09, while
number of samples than in any previous single                            in tropical Asia, A(H1N1)pdm09 was the domi-
year,17–19,21,22 with the majority of viruses received                   nant circulating strain followed by B/Victoria
(80%) from Australia. The high volume of sam-                            viruses.26
ples received correlated with a record number
of laboratory-confirmed influenza notifications                          Older adults are typically more affected in years
in Australia (313,365 cases) during the 2019                             when A(H3N2) viruses predominate, while
Australian influenza season.23 There was a con-                          younger populations are usually more affected
tinuation of intense inter-seasonal activity, with                       by A(H1N1)pdm09.27 Consistent with this
notifications of laboratory-confirmed influenza                          observation, high notification rates occurred in
at the end of May twelve times higher than dur-                          2019 among children aged 5–9 years (2,646 per
ing the same time period in the previous three                           100,000 population) and adults aged ≥ 85 years
years.24 The 2019 Australian season was charac-                          (2,370 per 100,000 population) in Australia.23
terised by an early peak and extended activity,                          Deaths associated with influenza and pneu-
with jurisdictions such as the Australian Capital                        monia were the ninth leading cause of death in
Territory and Tasmania displaying multiple                               2019, with 4,124 deaths recorded.28
peaks of activity.25 Unlike previous seasons,
where influenza samples received at the Centre                           Most of the influenza A(H1N1)pdm09 viruses
typically peaked in August, the Centre saw a                             received were antigenically and genetically sim-
dramatic increase in samples received early in                           ilar to the vaccine strain, A/Brisbane/02/2018,
the year, peaking in July 2019, with over 1,500                          which is in the 6B.1A/183P-1 genetic clade. A
samples received in that month alone.                                    number of A(H1N1)pdm09 viruses had amino
                                                                         acid changes in the HA gene, most significantly
The geographic spread of influenza around                                at residues 156 and 250; the former mutation
Australia began with a large epidemic of                                 has been previously associated with significant
A(H1N1)pdm09 in the Northern Territory,                                  antigenic changes in the haemagglutination
in December 2018. This was followed by large                             inhibition (HI) assay. These viruses were first
and sustained outbreaks of influenza in east-                            detected in Fiji and Brunei in early 2019 and
ern Australian jurisdictions, most notably                               were subsequently seen in some returned trav-
South Australia, in the first quarter of 2019.                           ellers from these regions to Australia. These
The Australian Capital Territory and Western                             antigenically-distinct viruses comprised 5.7%
Australia had comparatively lower levels of                              of the A(H1N1)pdm09 viruses tested and were
influenza notification but even these both had                           in the 6B.1A/183-P2 genetic clade. Mid-season
record notifications in 2019.25                                          vaccine effectiveness (VE) estimates suggest

12 of 16               Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021   health.gov.au/cdi
that vaccine protection in Australia for all age                      HA positions 162–164, and made up 64% of
groups was highest against A(H1N1)pdm09                               viruses genetically analysed at the Centre. The
viruses among both primary care (62%, 95%                             increase in circulation of this deletion variant
CI: 39,78) and hospitalised patients (70%, 95%                        also contributed to an increase in low-reacting
CI: 49, 82).29                                                        viruses in the HI assay, indicating a corre-
                                                                      sponding antigenic change compared to the
Antigenic analysis of A(H3N2) viruses showed                          vaccine virus. This led to the subsequent change
that the majority of viruses displayed similar                        in the recommendation for the 2020 Southern
antigenic characteristics to the cell-propagated                      Hemisphere B/Victoria-lineage vaccine compo-
vaccine strain, A/Switzerland/8060/2017. As                           nent to a B/Washington/02/2019-like triple HA
in previous years, there have been ongoing                            deletion virus.31 B/Yamagata viruses comprised
difficulties in the antigenic characterisation of                     only 10% of influenza B viruses analysed at the
A(H3N2) viruses. Evolutionary changes in this                         Centre, and all these viruses were antigenically
subtype continue to pose challenges in detect-                        and genetically similar to the vaccine strain,
ing antigenic changes using the HI assay.5,30                         B/Phuket/3073/2013.
Oseltamivir carboxylate was used in the HI
assay to prevent binding of the NA protein to red                     With the ongoing evolution of influenza viruses
blood cells, which resulted in a small number of                      and the absence of an effective universal vaccine,
A(H3N2) viruses having insufficient titre to be                       there remains a need for continuous influenza
tested in the HI assay (16% of A(H3N2) viruses                        surveillance and regular updating of influenza
isolated). The FRA continued to be used as com-                       vaccines. The work performed by the Centre in
plementary antigenic assay but remains time-                          Melbourne is part of the ongoing efforts of the
and labour-intensive. Of the viruses analysed                         WHO GISRS to perform these tasks in an effort
by FRA, 75% and 7%, respectively, were anti-                          to better control the disease burden of influenza.
genically similar to the cell- and egg-propagated
reference strain (A/Switzerland/8060/2017).

There were several distinct genetic clades
amongst circulating A(H3N2) viruses,
with the majority of viruses belonging to
the 3C.2a1b+131K HA clade, followed by
the 3C.2a1b+135K HA clade. Interestingly,
3C.2a2 viruses, which were represented by
the 2019 Southern Hemisphere vaccine strain
A/Switzerland/8060/2018, only accounted for
a very small proportion of circulating viruses
during 2019 and also led to a change in the
2020 Southern Hemisphere A(H3N2) vaccine
component to an A/South Australia/34/2019-
like virus.31

The majority of influenza B isolates analysed at
the Centre belonged to the B/Victoria-lineage
(86%). These B/Victoria-lineage viruses were
mostly antigenically similar to the vaccine
strain B/Colorado/6/2017; however, the major-
ity were phylogenetically similar to a new
variant that had previously emerged in the
Northern Hemisphere. This variant contained a
three-amino-acid deletion in the HA gene, from

health.gov.au/cdi     Commun Dis Intell (2018) 2021;45 (https://doi.org/10.33321/cdi.2021.45.43) Epub 16/8/2021    13 of 16
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