Molecular Respiratory Infection Pathogen Panel (RIPP) Testing

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Lab Management Guidelines                                                        V1.0.2021

                    Molecular Respiratory Infection
                    Pathogen Panel (RIPP) Testing
                                                                          MOL.CS.293.I
                                                                                v1.0.2021
Introduction

Molecular respiratory infection testing is addressed by this guideline.

Procedures addressed

The inclusion of any procedure code in this table does not imply that the code is under
management or requires prior authorization. Refer to the specific Health Plan's
procedure code list for management requirements.

Procedure(s) addressed by this                    Procedure code(s)
guideline
BioFire FilmArray Respiratory Panel (RP)          0098U
EZ
BioFire FilmArray Respiratory Panel (RP)          0099U
BioFire FilmArray Respiratory Panel 2             0100U
(RP2)
BioFire Respiratory Panel 2.1 including           0202U
SARS-CoV-2
BioFire FilmArray Pneumonia Panel                 0151U
ePlex Respiratory Pathogen (RP) Panel             0115U
ePlex Respiratory Pathogen Panel 2                0225U
Infectious agent detection by nucleic acid        87636
(DNA or RNA); severe acute respiratory
syndrome coronavirus 2 (SARSCoV-2)
(Coronavirus disease [COVID-19]) and
influenza virus types A and B, multiplex
amplified probe technique
Infectious agent detection by nucleic acid        87637
(DNA or RNA); severe acute respiratory
syndrome coronavirus 2 (SARSCoV-2)
(Coronavirus disease [COVID-19]),
influenza virus types A and B, and
respiratory syncytial virus, multiplex
amplified probe technique

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Procedure(s) addressed by this                    Procedure code(s)
guideline
Infectious agent detection by nucleic acid        87631
(DNA or RNA); respiratory virus (eg,
adenovirus, influenza virus, coronavirus,
metapneumovirus, parainfluenza virus,
respiratory syncytial virus, rhinovirus),
includes multiplex reverse transcription,
when performed, and multiplex amplified
probe technique, multiple types or
subtypes, 3-5 targets
Infectious agent detection by nucleic acid        87632
(DNA or RNA); respiratory virus (eg,
adenovirus, influenza virus, coronavirus,
metapneumovirus, parainfluenza virus,
respiratory syncytial virus, rhinovirus),
includes multiplex reverse transcription,
when performed, and multiplex amplified
probe technique, multiple types or
subtypes, 6-11 targets
Infectious agent detection by nucleic acid        87633
(DNA or RNA); respiratory virus (eg,
adenovirus, influenza virus, coronavirus,
metapneumovirus, parainfluenza virus,
respiratory syncytial virus, rhinovirus),
includes multiplex reverse transcription,
when performed, and multiplex amplified
probe technique, multiple types or
subtypes, 12-25 targets
QIAstat-Dx Respiratory SARS CoV-2                 0223U
Panel
Xpert Xpress SARSCoV-2/Flu/RSV                    0240U
(SARSCoV-2 & Flu targets only)
Xpert Xpress SARSCoV-2/Flu/RSV (all               0241U
                                                                                           RIPP
targets)

What is Respiratory Pathogens Panel Testing
Definition

Respiratory pathogens panel testing is the use of molecular technologies to detect
respiratory pathogens directly in a clinical sample.

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   In spite of the continued utilization of conventional diagnostic methods in clinical
    microbiology laboratories, the expanded availability of molecular methods for
    detection of pathogens directly in clinical specimens is changing the paradigm for
    diagnosis and management of patients with infectious diseases. One of the recent
    reasons for these changes has been the development of syndromic-based multiplex
    molecular panels, in this case, for respiratory presentations, with the ability to
    simultaneously detect, differentiate, and even subtype viral/bacterial pathogens in
    patient specimens.1
   Viral pathogens are the most common cause of respiratory tract infections.
    Seasonal influenza contributes to substantial morbidity and mortality each year in
    the United States. However, in a large portion of patients with respiratory tract
    infections, other viruses and non-cultivable organisms have been found to cause
    substantial morbidity and mortality.
   The ability to detect a large number pathogens rapidly and with high sensitivity and
    specificity has the potential to transform clinical microbiology as a continuing critical
    component of laboratory medicine. However, it is important to consider whether
    these tests should be front-line tests used for all patients with acute respiratory
    illness or whether their use should be limited to specific patients.

Test Information
Introduction

This section of the guideline contains information about testing for respiratory
pathogens.
   Respiratory panels may provide sample-to-answer results, using integrated nucleic
    acid extraction, amplification and detection with testing times of as little as 1 hour,
    typically using nasopharyngeal swab specimens. Several test systems have
    received FDA-clearance for the detection of respiratory tract pathogens, which has
    facilitated their rapid integration into routine testing. Other test platforms may
    include laboratory-validated panels that are customized for clinicians at their service
    clinical practice networks.
   The menu of analytes on several panels is for the first time providing access to            RIPP
    routine testing for pathogens that have previously been difficult to detect, or for
    which testing was only available at reference laboratories (i.e. norovirus,
    coronaviruses, Chlamydophila pneumoniae, Mycoplasma pneumoniae). These
    assays detect 12-20 pathogens and some include pathogens that typically cause
    different manifestations of infection, although they infect the same organ system.
   Analytically, the molecular assays usually exhibit comparative or superior detection
    rates compared to conventional methods which also result in an increased rate of
    diagnosis for affected patients.2,3 In addition, multiplex polymerase chain reaction
    (mPCR) molecular panels allow laboratories to consolidate testing for a broad
    range of pathogens from the same samples. This consolidation provides

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    opportunities to eliminate conventional testing methodologies, including direct
    fluorescent antibody (DFA) and cell culture for the detection of respiratory viruses.
   However, the fixed nature of the mPCR panels raises the concern that they might
    include pathogens causing infections with sufficiently clinical/epidemiological
    diversity, such that, in turn, simultaneous testing for those pathogens should be
    rare. Alternatively, the differences might be detectable by rapid, accurate and
    inexpensive tests (e.g. the Gram stain) that are part of routine testing. 4 It is
    reasonable to assert that negative test results for common pathogens should
    typically precede testing for uncommon pathogens.

Guidelines and Evidence
Introduction

The following section includes relevant guidelines and evidence pertaining to
respiratory pathogens panel testing.

American Society of Transplantation/Canadian Society of Transplantation

Manuel (2013) was modified from a previous guideline published in the American
Journal of Transplantation in 2009; 9(Suppl 4): S166–S172, and endorsed by American
Society of Transplantation/Canadian Society of Transplantation. 5 Guidelines were
again updated in 2019 by the American Society of Transplantation Infectious Diseases
Community of Practice:6
   “Since one cannot clinically distinguish disease caused by any of the respiratory
    viruses, diagnosis using broad ranging techniques should be considered
    particularly in the early period after transplantation or augmented
    immunosuppression and during respiratory viral season, particularly among lung
    transplant recipients.”
   “Nucleic acid amplification assay appear to be the most sensitive…and allow for
    simultaneous detection of a broad range of respiratory pathogens from a single
    sample and are therefore the preferred diagnostic testing method for
    immunocompromised patients. Multiplex PCR assays provide the advantage of
    identification of viruses not routinely found by conventional methods...”                  RIPP
Infectious Disease Society of America (IDSA)

In the 2018 IDSA practice guidelines for the “Diagnosis, Treatment, Chemoprophylaxis,
and Institutional Outbreak Management of Seasonal Influenza,” recommendations for
diagnostic testing include:7
   “Clinicians should use multiplex RT-PCR assays targeting a panel of respiratory
    pathogens, including influenza viruses, in hospitalized immunocompromosed
    patients (A-III).”

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   “Clinicians can consider using multiplex RT-PCR assays targeting a panel of
    respiratory pathogens, including influenza viruses, in hospitalized patients who are
    not immunocompromised if it might influence care (eg, aid in cohorting decisions,
    reduce testing, or decrease antibiotic use) (B-III).”

British Committee for Standards in Hematology

A joint working group established by the Hemato-oncology subgroup of the British
Committee for Standards in Hematology, the British Society for Bone Marrow
Transplantation and the UK Clinical Virology Network has reviewed the available
literature and made recommendations in 2016 for the diagnosis and management of
respiratory viral infections in patients with hematological malignancies or those
undergoing hematopoietic stem cell transplantation. To illustrate: 8
   “It is currently recommended that the diagnosis of respiratory viral infections is
    made by quantitative nucleic acid amplification tests (NAATs), generically referred
    to hereafter as PCR; clinicians should be able to liaise with their virology laboratory
    colleagues regarding the interpretation of PCR results … A panel of viruses should
    be included for PCR testing, including parainfluenza type 4.”

German Society for Haematology and Medical Oncology

A panel of 18 clinicians from the Infectious Diseases Working Party of the German
Society for Haematology and Medical Oncology convened to assess the available
literature and provide 2016 recommendations on the management of community
acquired respiratory virus infections including influenza, respiratory syncytial virus
(RSV), parainfluenza virus (PIV), human metapneumovirus (hMPV) and
adenovirus. Two relevant excerpts include:9
   “Most data on this topic originate from patients following allogeneic stem cell
    transplantation (allo-SCT), and we know little about community-acquired respiratory
    virus (CARV) infections in cancer patients outside the setting of allo-SCT. However,
    in recent years increasing evidence has been gathered about other cancer patients,
    revealing clinical relevance of CARV infections in non-transplant patients.
    Therefore, this guideline discusses CARV infections in all cancer patients with
    ongoing relevant immunosuppression. It is left to the treating physician to assess
    the degree and relevance of immunosuppression in the individual patient.”                    RIPP
   “In the era of multiplex-test kits, it is difficult to make a definite recommendation with
    regard to which viruses should be looked for. In the absence of any reliable data
    regarding this question, the panel feels that it is wise to search for influenza, RSV,
    PIV and viruses currently prevalent in the local environment in all
    immunosuppressed cancer patients presenting with symptoms. Patients with more
    severe disease (for example pneumonia or critical illness) may have the panel
    broadened to include hMPV and adenovirus and even viruses that only rarely cause
    lower respiratory tract infections like rhinovirus and coronavirus. However, evidence
    for this approach is low and it is strongly advisable to define local guidelines on this
    topic.”

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Fourth European Conference on Infections in Leukemia

A working group of the Fourth European Conference on Infections in Leukemia (ECIL-
4) 2011 reviewed the literature on community-acquired respiratory virus (CARV),
graded the available quality of evidence, and made the relevant diagnostic
recommendations according to the Infectious Diseases Society of America (IDSA)
grading system:10
   First-line diagnostic testing should be performed for influenza A and B, RSV, and
    human parainfluenza viruses (HPIV) (IDSA Grade A II).
   Testing for other CARVs should be considered according to risk of exposure and
    the local epidemiology, or if testing for the firstline CARVs is negative (IDSA Grade
    B III).

Expert Written and Peer Reviewed Articles

There have been additionally referenced indications for the use of (typically viral)
respiratory pathogen panels, such as for adult patients appearing acutely ill, who are
potential hospital admissions, where, for example, such panel testing would be ordered
in the emergency department (ED). To illustrate, two randomized controlled studies
have described some possible favorable outcomes in the ED:
   Brendish (2017)11 where respiratory viral panel testing did not ... “reduce the
    proportion of patients treated with antibiotics. However, the primary outcome
    measure failed to capture differences in antibiotic use because many patients were
    started on antibiotics before the results of point-of-care testing (POCT) could be
    made available. Although POCT was not associated with a reduction in the duration
    of antibiotics overall, more patients in the POCT group received single doses or
    brief courses of antibiotics than did patients in the control group. POCT was also
    associated with a reduced length of stay and improved influenza detection and
    antiviral use, and appeared to be safe.”
   Brittain-Long (2011)2 found that ... “In the group of patients randomised for a rapid
    result, 4.5% (9 of 202) of patients received antibiotics at the initial visit, compared to
    12.3% (25 of 204) (P = 0.005) of patients in the delayed result group. At follow-up,
    there was no significant difference between the groups: 13.9% (28 of 202) in the
    rapid result group and 17.2% (35 of 204) in the delayed result group (P = 0.359),             RIPP
    respectively.” … with the conclusion that …“Access to a rapid method for etiologic
    diagnosis of acute respiratory tract infections (ARTIs) may reduce antibiotic
    prescription rates at the initial visit in an outpatient setting. To sustain this effect,
    however, it seems necessary to better define how to follow and manage the patient
    according to the result of the test, which warrants further investigation.”
Furthermore, critically-ill adult patients, particularly intensive care unit (ICU) patients,
lack the same evidentiary level for metrics such as the reduction of unnecessary
antibiotic use, which is a major cause of morbidity in hospitalized patients. However,
case series studies make a convincing case that respiratory viral pathogens are of
considerable relevance in the ICU setting. To illustrate, Choi (2012) 12 found that viral

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infection is common in adult patients with severe pneumonia. About one-third of
patients with severe community-acquired pneumonia or healthcare-associated
pneumonia had viral infections, and the mortality from viral infection and bacterial
infection was comparable. The viral agents involved in descending order of prevalence
were rhinovirus, parainfluenza virus (Types 3, 1, 2, and 4, respectively), hMPV,
influenza, RSV, and, more infrequently, cytomegalovirus, human coronavirus,
adenovirus, and enterovirus. Furthermore, Voiriot (2016) 13 observed a relatively more
complicated course among ICU patients with mixed bacterial and viral respiratory
infections.
Outcome data for use of multiplex panels in adult ambulatory patients is generally more
mixed. For example, Green et al. (2016) showed that use of a multiplex panel (Biofire
FilmArray v1.7 respiratory panel) in outpatient adults (VA patients) led to increased
rates of oseltamivir and decreased rates of antibiotics for patients diagnoses with
influenza, but there was no significant difference in antibiotic prescription rates
between patients who tested negative and those who had a non-influenza virus—
suggesting a targeted influenza diagnostic may have been adequate in their
population.14 When specifically evaluating patients at an ambulatory cancer center,
however, Krantz et al. (2019) found that multiplex viral testing on day 0 decreased the
risk of antibiotic prescriptions by half compared to patients who were not tested on day
0.15
It should be noted that the utility of multiplex testing for each institution and patient
population should be interpreted in the context of the turn-around-time (TAT) of the
assay(s) available. Wabe et al (2019) evaluated outcomes of patients presenting to the
emergency department before and after a transition from a standard multiplex PCR
performed at a centralized laboratory (TAT of 26.7 hours; 16 viruses) to a rapid
hospital-based assay that only detects influenza A, influenza B, and RSV (TAT 2.4
hours).16 A small, but statistically significant, decrease in hospital admissions was
noted after implementing the more limited, but rapid assay
Finally, however, there were no substantive peer-reviewed full articles which addressed
the relative clinical impact of ordering respiratory pathogen panels, with differing
numbers of infectious targets.

Criteria
                                                                                             RIPP
Introduction

Requests for molecular respiratory infection pathogen panel (RIPP) testing using
procedure codes are reviewed using the following clinical criteria.

87631, 87632, and 87633

The presence of acute respiratory symptoms in members 17 years of age or younger,
OR
The presence of acute respiratory symptoms in members of any age who are:

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   Immunocompromised (as defined by ICD-10 codes), OR
   Immunocompetent and receiving care for their acute respiratory symptoms in a
    hospital setting as evidenced by the following

    o Place of service code on the claim is: 19, 22, or 23 , or
    o Bill type code on the claim is: 13X or 14X, OR

The following is a contraindication to RIPP testing in members 18 years of age or older:
   Presence of respiratory symptoms that suggest a specific respiratory pathogen in
    an immunocompetent adult.
Molecular RIPP testing is limited to the minimum number of targets needed for
therapeutic decision making. When ordering any configuration of infectious disease
targets, whether using RIPP or conventional testing, the medical record should clearly
indicate the differential diagnosis of possible microorganisms based upon member
history and presenting signs/symptoms.
It is not necessary to repeat a respiratory pathogen panel to ensure a causative
organism is cleared. If test of cure is indicated for a particular organism, individual
organism testing should be used. Therefore, repeat testing of any panel within a two
week time frame will not be reimbursed.

0098U, 0099U, 0100U, 0115U, and 0151U

These procedure codes are considered investigational and/or experimental and,
therefore, not eligible for reimbursement.

Billing and reimbursement

   No more than one respiratory virus panel should be necessary on a single date of
    service. Therefore, only one unit of the same panel code will be reimbursable and
    two different panel codes (e.g. 87631, 87632, 87633, 0202U, or 0223U) cannot be
    billed on the same date of service.
   More than one type of test for the same organism will not be reimbursable for the
    same date of service (e.g., 87631 and 87634 may not be billed together).
   A code representing only the minimum panel necessary to detect the necessary
                                                                                                RIPP
    targets should be billed. If the laboratory’s testing platform consists solely of a panel
    of multiple targets, yet only a subset of the organisms are considered medically
    necessary based on the above criteria, the lab may request reimbursement for that
    subset of organisms using a procedure code that does not represent all organisms
    included on the panel (e.g., bill 87632 if only 8 targets are necessary even if 12 or
    more targets were tested as part of a panel usually billed with 87633).

Note   Inpatient services are beyond the scope and domain of this guideline.

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Although outbreak investigations may sometimes require use of RIPP testing, the
public health evaluations of such outbreaks are beyond the scope and domain of this
guideline.

ICD10 codes

ICD10 codes in this section may be used to support medical necessity as described in
the above criteria.
ICD10 Codes Indicating Cancer, Transplant, or Other Immunocompromise

ICD10 Code or Range                               Description
B20                                               Human immunodeficiency virus [HIV]
                                                  disease
B59                                               Pneumocystosis
C00.X-C96.X                                       Malignant neoplasms
D37.X-D48.X                                       Neoplasms of uncertain behavior,
                                                  polycythemia vera and myelodysplastic
                                                  syndromes
D60.X-D64.X                                       Aplastic and other anemias and other
                                                  bone marrow failure syndromes
D70.X-D77                                         Other disorders of blood and blood-
                                                  forming organs
D80.X-D89.X                                       Certain disorders involving the immune
                                                  mechanism
E40-E46                                           Malnutrition
I12.0                                             Hypertensive chronic kidney disease with
                                                  stage 5 chronic kidney disease or end
                                                  stage renal disease
I13.11                                            Hypertensive heart and chronic kidney
                                                  disease without heart failure, with stage 5
                                                  chronic kidney disease, or end stage renal
                                                  disease                                        RIPP
I13.2                                             Hypertensive heart and chronic kidney
                                                  disease with heart failure and with stage 5
                                                  chronic kidney disease, or end stage renal
                                                  disease
K91.2                                             Postsurgical malabsorption, not elsewhere
                                                  classified
M35.9                                             Systemic involvement of connective
                                                  tissue, unspecified

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ICD10 Code or Range                               Description
N18.5                                             Chronic kidney disease, stage 5
N18.6                                             End stage renal disease
T86.X                                             Complications of transplanted organs and
                                                  tissue
Z48.2X                                            Encounter for aftercare following organ
                                                  transplant
Z49.X                                             Encounter for care involving renal dialysis
Z94.X                                             Transplanted organ and tissue status
Z99.2                                             Dependence on renal dialysis

References
Introduction

The following references are cited in the guideline.

1. American Society for Microbiology. Multiplex Array White Paper: Clinical Utility of
   Multiplex Tests for Respiratory and Gastrointestinal Pathogens.
   https://www.asm.org/index.php/statements-and-testimony/item/6691-wp-multiplex
   Published July 18, 2017. Accessed July 18, 2017.
2. Brittain-Long R, Westin J, Olofsson S, Lindh M, Andersson LM. Access to a
   polymerase chain reaction assay method targeting 13 respiratory viruses can
   reduce antibiotics: a randomised, controlled trial. BMC Med. 2011;9:44.
3. Johansson N, Kalin M, Tiveljung-Lindell A, Giske CG, Hedlund J. Etiology of
   community-acquired pneumonia: increased microbiological yield with new
   diagnostic methods. Clin Infect Dis. 2010;50(2):202-209.
4. Schreckenberger PC, McAdam AJ. Point-Counterpoint: Large Multiplex PCR
   Panels Should Be First-Line Tests for Detection of Respiratory and Intestinal
   Pathogens. J Clin Microbiol. 2015;53(10):3110-3115.
                                                                                                  RIPP
5. Manuel O, Estabrook M. RNA respiratory viruses in solid organ transplantation. Am
   J Transplan. 2013;13 Suppl 4:212-219.
6. Manuel O, Estabrook M, American Society of Transplantation Infectious Diseases
   Community of Practice. RNA respiratory viral infections in solid organ transplant
   recipients: Guidelines from the American Society of Transplantation Infectious
   Diseases Community of Practice. Clin Transplant. 2019;33(9):e13511.
7. Uyeki T, Bernstein H, Bradley J, et al. Clinical practice guidelines by the Infectious
   Diseases Society of America: 2019 update on diagnosis, treatment,
   chemoprophylaxis, and institutional outbreak management of seasonal influenza.
   Clin Infect Dis. 2019;68(6):e1-e47.

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8. Dignan FL, Clark A, Aitken C, et al. BCSH/BSBMT/UK clinical virology network
   guideline: diagnosis and management of common respiratory viral infections in
   patients undergoing treatment for haematological malignancies or stem cell
   transplantation. Br J Haematol.2016;173(3):380-393.
9. von Lilienfeld-Toal M, Berger A, Christopeit M, et al. Community acquired
   respiratory virus infections in cancer patients-Guideline on diagnosis and
   management by the Infectious Diseases Working Party of the German Society for
   haematology and Medical Oncology. Eur J Cancer (Oxford, England : 1990).
   2016;67:200-212.
10. Hirsch HH, Martino R,Ward KN, Boeckh M, Einsele H, Ljungman P. Fourth
    European Conference on Infections in Leukaemia (ECIL-4): guidelines for
    diagnosis and treatment of human respiratory syncytial virus, parainfluenza virus,
    metapneumovirus, rhinovirus, and coronavirus. Clin Infect Dis. 2013;56(2):258-
    266.
11. Brendish NJ, Malachira AK, Armstrong L, et al. Routine molecular point-of-care
    testing for respiratory viruses in adults presenting to hospital with acute respiratory
    illness (ResPOC): a pragmatic, open-label, randomised controlled trial. Lancet.
    2017;5(5):401-411.
12. Choi SH, Hong SB, Ko GB, et al. Viral infection in patients with severe pneumonia
    requiring intensive care unit admission. Am J Respir Crit Care Med.
    2012;186(4):325-332.
13. Voiriot G, Visseaux B, Cohen J, et al. Viral-bacterial coinfection affects the
    presentation and alters the prognosis of severe community-acquired pneumonia.
    Crit Care (London, England). 2016;20(1):375.
14. Green DA, Hitoaliaj L, Kotansky B, Campbell SM, Peaper DR. Clinical utility of on-
    demand multiplex respiratory pathogen testing among adult outpatients. J Clin
    Microbiol. 2016;54(12):2950-2955.
15. Krantz EM, Zier J, Stohs E, et al. Antibiotic prescribing and respiratory viral testing
    for acute upper respiratory infections among adult patients at an ambulatory cancer
    center. Clin Infect Dis Off Publ Infect Dis Soc Am. May 2019.
    doi:10.1093/cid/ciz409 [Epup ahead of print].
16. Wabe N, Li L, Lindeman R, et al. The impact of rapid molecular diagnostic testing
    for respiratory viruses on outcomes for emergency department patients. Med J               RIPP
    Aust. 2019;210(7):316-320.

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