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

Abstract

Background Our understanding of the co-circulation of infrequently targeted respiratory pathogens and their contribution to symptoms during the 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-SARS-CoV-2/influenza/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 re-testing two cohorts of specimens that were 1) collected from symptomatic patients and 2) received limited respiratory pathogen testing. The first cohort was patients 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.

The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads

“…The SARS-CoV-2 positivity rate increased markedly in December 2021 (symptomatic, 25.5%, Table 2 and Figure 2 a). The large increase in SARS-CoV-2 positivity in the month of December was the highest recorded since the beginning of the pandemic (Figure S1a and 22 ). The spike in SARS-CoV-2 positivity was particularly evident during the last two weeks of December for both symptomatic and asymptomatic patients ( Figure 2 a).…”

Evaluation of the respiratory NeuMoDx™ Flu A-B/RSV/SARS-CoV-2 Vantage and Alinity m Resp-4-Plex assays

“…The respiratory virus season of 2021- 2022 has been particularly challenging due to the marked increase in symptomatic infections associated with the surge of SARS-CoV-2 positivity rates caused by the widespread prevalence of the Omicron variant [2] . The associated circulation of influenza viruses that started to increase in the beginning of December 2021 as well as RSV that showed a marked increase especially in July and August 2021 [1] led to an increase in the testing demand for SARS-CoV-2, influenza viruses, and RSV. Different commercial molecular test options that multiplexed influenza and RSV with SARS-CoV-2 have received the emergency use authorization (EUA) by the FDA.…”

“…The diagnostic laboratory testing of influenza and RSV increases during the seasons of their circulation. The COVID-19 pandemic impacted the circulation of respiratory viruses, including influenza and RSV, associated with measures of mitigating the spread of SARS-CoV-2 [1] . Upon relaxing the infection control measures, a rebound in respiratory viruses was notable after May 2021 with marked increases in enterovirus/rhinovirus and RSV [1] .…”

“…The COVID-19 pandemic impacted the circulation of respiratory viruses, including influenza and RSV, associated with measures of mitigating the spread of SARS-CoV-2 [1] . Upon relaxing the infection control measures, a rebound in respiratory viruses was notable after May 2021 with marked increases in enterovirus/rhinovirus and RSV [1] . The first detection of influenza in our system in 2021 was on October 27 th followed by a slow increase in the number of cases to reach an average positivity of 3% in the month of December.…”

Epidemiology of rhinovirus under the COVID‐19 pandemic in Guangzhou, China, 2020

“…Studies conducted in Shanghai, China, America, and German showed that HRV stayed low in the first quarter of 2020, and raised rapidly in June, matches our study, and observed relatively higher morbidity in the rest of the year. 18 , 19 , 20 , 21 Another study 22 conducted in Southampton, UK, gave a theory that the HRV was mainly found in children and adolescents who were the major reservoir for HRV infection, social distancing and face masks are not effective in preventing transmission of HRV, with “ Back‐to‐School Upper Respiratory Infection ” effect, 23 the risk of HRV transmission surges after schools reopening. On the other hand, Dr. Leung et al 24 conducted experiments and proved that there was no significant difference in filtering or protection effect of HRV between wearing a face mask or not, indicating that wearing masks cannot effectively protect the population from the HRV infection.…”