The Effect of SARS-CoV-2 Mitigation Strategies on Seasonal Respiratory Viruses: A Tale of Two Large Metropolitan Centers in the United States

Abstract To assess the impact of the SARS-CoV-2 pandemic on seasonal respiratory viruses, absolute case counts and viral reproductive rates from 2019-2020 were compared against previous seasons. Our findings suggest that the public health measures implemented to reduce SARS-CoV-2 transmission significantly reduced the transmission of other respiratory viruses.

hemisphere in January 2020 overlapped with the peak circulation of seasonal respiratory viruses that include influenza A and B and respiratory syncytial virus (RSV). Like SARS-CoV-2, these viruses are also spread primarily through droplet and contact transmission routes, with concern that cocirculating respiratory pandemics could further stress our healthcare systems and economy [2,3].
The danger represented by the unchecked spread of SARS-CoV-2 prompted a massive rollout of population-level non-pharmaceutical interventions (NPIs) to curb transmission, including stay-athome orders, the closure of schools and retail spaces, mandated face masks in public, and encouragement of social distancing and hand hygiene. Studies from Hong Kong, France, Japan, Singapore and Australia have shown these measures coincided with a decline in the number of cases of the seasonal respiratory viruses over the same time period, as compared to prior seasons [3][4][5][6][7]. A similar trend occurred in the U.S., with the number of people with influenza-like illness (ILI) [8] for the 2019-2020 season decreasing earlier than expected as compared to other influenza seasons [9].
In this study, we examined the effect of NPIs on the rates of infection from influenza A, influenza B and RSV in two large academic centers located in Atlanta, Georgia and Boston, Massachusetts from January through May 2020. The heterologous impact of mitigation strategies has important implications for clinicians and laboratories preparing for future respiratory virus seasons. The dynamics of influenza, RSV, and SARS-CoV-2 epidemiology are complex, and the interplay between these respiratory viruses will become increasingly important to dissect as a new influenza season emerges in the fall of 2020. Globally, the effects of decreased influenza cases from January to May 2020, due to either decreased transmission or decreased surveillance, may confound the ability to accurately predict which strains will be circulating in the fall. With decreased international travel and border restrictions, there may also be a change in the temporal dynamics of influenza illness in 2020-2021, and the circulating strains may differ from those predicted in February 2020. Further study is warranted to determine the downstream effects that SARS-CoV-2 will have on influenza transmission, epidemiological trends, and influenza strain selection for future influenza vaccines.
Limitations include the possibility of decreased reporting of influenza (Supplemental Figure 2 and 3) and RSV due to a decline in overall outpatient clinic, preservation of viral media and equipment for SARS-CoV-2 testing, and transitions in hospitals to prioritize SARS-CoV-2 testing over other viral diagnostics for hospitalized patients [10]. We were unable to distinguish inpatient from outpatient testing in our cohort, and there may have been decreased medical care seeking for less severe disease. Complex viral factors and dynamics between circulating SARS-CoV-2 and influenza viruses may have also influenced this trend. The phenomenon of respiratory virus "interference" has been described for epidemics of influenza and other respiratory viruses, in which one epidemic delays the start or accelerates the end of the other viral epidemic [11][12][13]. This was an ecological analysis that cannot determine causality; future studies should further investigate these variables that likely contribute to the effects described.
In summary, the data demonstrate that NPIs are likely effective in reducing both influenza and SARS-CoV-2 transmission. Concurrent epidemics of influenza and SARS-CoV-2 have the potential to result in diagnostic confusion, and significant morbidity and mortality and could overwhelm the healthcare system. Consequently, NPIs, in addition to widespread administration of influenza vaccination, will be important public health tools to deploy to mitigate the threat of these respiratory viruses. Ongoing diagnostic and surveillance efforts for influenza, RSV and SARS-CoV-2 must be maintained to further explore the transmission mechanisms and interplay between these respiratory viruses.