The circulation of Non-SARS-CoV-2 respiratory viruses and coinfections with SARS-CoV-2 during the surge of the Omicron variant.

BACKGROUND: In December 2021, the SARS-CoV-2 Omicron variant displaced the Delta variant and caused an unprecedented spike in the numbers of COVID-19 cases. This study reports the positivity rates of circulating non-SARS-CoV-2 respiratory viruses and evaluates coinfections of these viruses with SARS-CoV-2 during the Omicron surge. METHODS: Data from the multiplex respiratory panels used for diagnosis at the Johns Hopkins Microbiology Laboratory were used to assess positivity rates and respiratory virus coinfections in the time frame between November 2021 and February 2022. Clinical presentations and outcomes were assessed in the cohort of 46 patients who had SARS-CoV-2 coinfections with other respiratory viruses. RESULTS: Between November 2021 and February 2022, the high positivity of SARS-CoV-2 outcompeted enterovirus/rhinovirus and other circulating respiratory viruses and was associated with a notable decrease in influenza A infections. Coinfections represented 2.3% of the samples tested by the extended multiplex respiratory panel. SARS-COV-2 coinfections represented 25% of the coinfections in this time frame and were mostly SARS-COV-2/enterovirus/rhinovirus. Of the SARS-CoV-2 coinfection cohort, 3 patients were hospitalized and were coinfected with influenza-A (2) or RSV (1). Cough and shortness of breath were the most frequent symptoms (29%) followed by fever (28%). CONCLUSIONS: The SARS-CoV-2 Omicron surge was associated with a change in the circulation of other respiratory viruses. Coinfections were most prevalent with viruses that showed the highest positivity in this time frame.

Circulation of Non-SARS-CoV-2 Respiratory Pathogens and Coinfection with SARS-CoV-2 Amid the COVID-19 Pandemic.

BACKGROUND: Our understanding of the cocirculation of infrequently targeted respiratory pathogens and their contribution to symptoms during the coronavirus disease 2019 (COVID-19) pandemic is currently limited. This research aims at (1) understanding the epidemiology of respiratory pathogens since the start of the pandemic, (2) assessing the contribution of non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/influenza/respiratory syncytial virus (RSV) respiratory pathogens to symptoms, and (3) evaluating coinfection rates in SARS-CoV-2-positive patients, both vaccinated and unvaccinated. METHODS: Retrospective analysis of respiratory pathogens identified by the Johns Hopkins Diagnostic Laboratory between December 2019 and October 2021 was performed. In addition, we assessed the contribution of respiratory pathogens other than SARS-CoV-2 to symptomatic disease by retesting 2 cohorts of specimens that were (1) collected from symptomatic patients and (2) received limited respiratory pathogen testing. The first cohort was patients who tested negative by the standard-of-care SARS-CoV-2/influenza/RSV testing. The second was a cohort of SARS-CoV-2-positive, symptomatic, fully COVID-19 immunized and unimmunized patients. RESULTS: Between December 2019 and October 2021, a total of 11 806, 62 829, and 579 666 specimens were tested for an extended respiratory panel, influenza/RSV with or without SARS-CoV-2 panel, or SARS-CoV-2, respectively. Positivity rates of different targets differed between different months and were impacted by the COVID-19 pandemic. The SARS-CoV-2-negative cohort had 8.5% positivity for other respiratory pathogens that included primarily enterovirus/rhinovirus (5.8%). In the SARS-CoV-2-positive cohort, no other respiratory pathogens were detected. CONCLUSIONS: The COVID-19 pandemic impacted the circulation of certain respiratory pathogens. Other respiratory viral pathogens were associated with symptomatic infections; however, coinfections with SARS-CoV-2 were highly uncommon.

Clinical performance of the GenMark Dx ePlex respiratory pathogen panels for upper and lower respiratory tract infections.

The GenMark Dx ePlex Respiratory Pathogen Panel (RP) is a multiplexed nucleic acid test for the qualitative detection of common viral and a few bacterial causes of respiratory tract infections. The ePlex RP has received FDA clearance for nasopharyngeal swab (NPS) specimens collected in viral transport media. In this study, we evaluated the performance of the ePlex RP panel in comparison to the NxTAG Respiratory Pathogen Panel (NxTAG-RPP) from Luminex in use in our laboratory, not only for NPS but also for bronchoalveolar lavage specimens (BAL). We also evaluated the impact of implementing the ePlex RP on the test turn-around time (TAT). The newest panel from GenMark Dx, the ePlex Respiratory Pathogen Panel 2 (RP2), which added the SARS-CoV-2 target to the RP was also evaluated for NPS. Verification of the performance of the ePlex RP for both NPS and BAL showed 93.3 % and 84.9 % total agreement with the NxTAG-RPP respectively. An overall comparison of the TAT after implementing the ePlex RP as compared to the NxTAG-RPP assay showed an average decrease of almost seven-fold.

Multicenter evaluation of the NeuMoDx™ SARS-CoV-2 Test.

The SARS-CoV-2 virus has caused millions of confirmed COVID-19 cases worldwide and hundreds of thousands of deaths in less than 6 months. Mitigation measures including social distancing were implemented to control disease spread, however, thousands of new cases continue to be diagnosed daily. To resume some suspended social activities, early diagnosis and contact tracing are essential. To meet this required diagnostic and screening capacity, high throughput diagnostic assays are needed. The NeuMoDx™ SARS-CoV-2 assay, performed on a NeuMoDx molecular system, is a rapid, fully automated, qualitative real-time RT-PCR diagnostic test with throughput of up to 288 tests in an 8 -h shift. The assay received emergency use authorization from the FDA and is used in some large testing centers in the US. This paper describes the analytical and clinical performance of the assay at three centers: Johns Hopkins Hospital, St. Jude Children's Research Hospital, and the Wadsworth Center.

Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus?

Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.

Comparing the analytical performance of three SARS-CoV-2 molecular diagnostic assays.

In December 2019, a novel coronavirus (SARS-CoV-2) was first isolated from Wuhan city, China and within three months, the global community was challenged with a devastating pandemic. The rapid spread of the virus challenged diagnostic laboratories to rapidly develop molecular diagnostic methods. As SARS CoV-2 assays became available for testing on existing molecular platforms, laboratories devoted unprecedented energy and resources into evaluating the analytical performance of the new tests and in some cases developed their own diagnostic assays under FDA-EUA guidance. This study compares the validation of three different molecular assays at the Johns Hopkins Molecular Virology laboratory: the RealStar® SARS-CoV-2 RT-PCR, ePlex® SARS-CoV-2, and the CDC COVID-19 RT-PCR tests. Overall, our studies indicate a comparable analytical performance of the three assays for the detection of SARS-CoV-2.