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.