Changes in Influenza and Other Respiratory Virus Activity During the COVID-19 Pandemic — United States, 2020–2021

We identified seasonal human coronaviruses, influenza viruses and rhinoviruses in exhaled breath and coughs of children and adults with acute respiratory illness. Surgical face masks significantly reduced detection of influenza virus RNA in respiratory droplets and coronavirus RNA in aerosols, with a trend toward reduced detection of coronavirus RNA in respiratory droplets. Our results indicate that surgical face masks could prevent transmission of human coronaviruses and influenza viruses from symptomatic individuals. Show more

After recognition of widespread community transmission of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), by mid- to late February 2020, indicators of influenza activity began to decline in the Northern Hemisphere. These changes were attributed to both artifactual changes related to declines in routine health seeking for respiratory illness as well as real changes in influenza virus circulation because of widespread implementation of measures to mitigate transmission of SARS-CoV-2. Data from clinical laboratories in the United States indicated a 61% decrease in the number of specimens submitted (from a median of 49,696 per week during September 29, 2019–February 29, 2020, to 19,537 during March 1–May 16, 2020) and a 98% decrease in influenza activity as measured by percentage of submitted specimens testing positive (from a median of 19.34% to 0.33%). Interseasonal (i.e., summer) circulation of influenza in the United States (May 17–August 8, 2020) is currently at historical lows (median = 0.20% tests positive in 2020 versus 2.35% in 2019, 1.04% in 2018, and 2.36% in 2017). Influenza data reported to the World Health Organization’s (WHO’s) FluNet platform from three Southern Hemisphere countries that serve as robust sentinel sites for influenza from Oceania (Australia), South America (Chile), and Southern Africa (South Africa) showed very low influenza activity during June–August 2020, the months that constitute the typical Southern Hemisphere influenza season. In countries or jurisdictions where extensive community mitigation measures are maintained (e.g., face masks, social distancing, school closures, and teleworking), those locations might have little influenza circulation during the upcoming 2020–21 Northern Hemisphere influenza season. The use of community mitigation measures for the COVID-19 pandemic, plus influenza vaccination, are likely to be effective in reducing the incidence and impact of influenza, and some of these mitigation measures could have a role in preventing influenza in future seasons. However, given the novelty of the COVID-19 pandemic and the uncertainty of continued community mitigation measures, it is important to plan for seasonal influenza circulation in the United States this fall and winter. Influenza vaccination of all persons aged ≥6 months remains the best method for influenza prevention and is especially important this season when SARS-CoV-2 and influenza virus might cocirculate ( 1 ). Data from approximately 300 U.S. clinical laboratories located throughout all 50 states, Puerto Rico, Guam, and the District of Columbia that participate in virologic surveillance for influenza through either the U.S. WHO Collaborating Laboratories System or the National Respiratory and Enteric Virus Surveillance System* were used for this analysis. Clinical laboratories primarily test respiratory specimens for diagnostic purposes, and data from these laboratories provide useful information on the timing and intensity of influenza activity. The median number of specimens tested per week and the median percentage of samples testing positive for influenza during September 29, 2019–February 29, 2020 (surveillance weeks 40–9, the period before the March 1, 2020 declaration of a national emergency related to COVID-19 † ) were compared with those tested during March 1–May 16, 2020 (weeks 10–20 after the declaration); data from three previous influenza seasons are presented as a comparison. To assess influenza virus activity in the Southern Hemisphere, influenza laboratory data from clinical and surveillance platforms reported from Australia, Chile, and South Africa to WHO’s FluNet § platform were analyzed. For each country, the percentage of samples testing positive for influenza for April–July (weeks 14–31) for four seasons (2017–2020) are presented. Selected measures implemented to respond to COVID-19 in these countries were ascertained from government websites. All data used were in the public domain. In the United States, influenza activity (measured by percentage of respiratory specimens submitted for influenza testing that yielded positive results) began to increase in early November 2019, and >20% of specimens were positive during December 15, 2019–March 7, 2020 (weeks 51–10), after which activity declined sharply (Figure 1). Percent positivity peaked on week 6 at 30.25% and decreased 14.90% by week 9, compared with an 89.77% decrease during weeks 10–13. By the week of March 22, 2020 (week 13), when the number of samples tested remained very high, percent positivity dropped to 2.3%, and since the week of April 5, 2020 (week 15), has remained 20% to 2.3% and has remained at historically low interseasonal levels (0.2% versus 1–2%). Data from Southern Hemisphere countries also indicate little influenza activity. What are the implications for public health practice? Interventions aimed against SARS-CoV-2 transmission, plus influenza vaccination, could substantially reduce influenza incidence and impact in the 2020–21 Northern Hemisphere season. Some mitigation measures might have a role in reducing transmission in future influenza seasons. Show more

To the Editor—Yeoh et al reported the dramatic impact of public health measures introduced during the coronavirus disease 2019 (COVID-19) pandemic on influenza and respiratory syncytial virus (RSV) detections in Western Australian (WA) children [1]. Here, we present data from ongoing local prospective surveillance. Following the end of winter, there has been a persistent absence of severe acute respiratory syndrome coronavirus 2 community transmission and no increase in influenza detections. Limited physical distancing measures have remained in place, with largely no restrictions on gathering sizes and no mandate for wearing masks [2]. Schools have remained open. Strict quarantine for overseas arrivals has been maintained, with a persistent marked decrease in visitor numbers compared with previous numbers [3]. Border restrictions for travelers from other states within Australia have been reduced as of 14 November 2020, with quarantine not required for travelers from states with no community severe acute respiratory syndrome coronavirus 2 transmission [4]. Similar to the previous report laboratory data prospectively collected as part of routine regional public health surveillance were collated per week from January 2012 to 13 December 2020. Cases were defined as detections of RSV by validated nucleic acid amplification test or antigen detection kits in children (<16 years of age) in the metropolitan area. Laboratory results were provided by PathWest Laboratory Medicine, the only public pathology provider to the state. Samples were drawn from all public hospitals and emergency departments. Average epidemic curves for the period 2012 to 2019 were calculated using a World Health Organization–described method [5]. Median age was compared using 2-sample Wilcoxon test. As demonstrated in Figure 1, RSV activity increased from late September, in the setting of relaxed physical distancing recommendations, ahead of the opening of interstate borders. Case numbers have further increased, exceeding the median seasonal peak from 2012 to 2019. This has been observed without any significant change in testing practices. The median patient age this year was 18.4 months, significantly higher than the upper range between 2012 and 2019 (7.3–12.5 months) (P < .001). Figure 1. Respiratory syncytial virus detection in children from metropolitan Western Australian up to week 50 of 2020, in the context of COVID-19 restrictions, compared to average epidemic curve (2012–2019). Borders closed – week 12 – international borders closed to all nonresidents; 14-day quarantine required for all arrivals. Period 1 (weeks 14–17): statewide stay-at-home restrictions in place with school holidays extended; borders closed to inter-state travelers (week 14). Period 2 (weeks 18–26): restrictions sequentially lifted, allowing gatherings of 10 (week 18), 20 (week 21), and 100 (week 24) people; schools reopened with increased cleaning and some physical distancing measures. Period 3 (weeks 27–47): majority of local restrictions removed, except the limitation of major sport and entertainment venues to 50% capacity; schools returned to all normal activities. Period 4 (weeks 47–50) relaxation of state border restrictions. Average epidemic curve: 2012–2019. Abbreviation: EYTD, end of year to date. These data demonstrate the fragility of RSV control and the critical impact of physical distancing and respiratory hygiene practices. The rise in numbers and change in median age suggest that the expanded cohort of RSV-naïve patients, including an increased number of older children coupled with waning population immunity [6], may have contributed to this marked resurgence. Notably, RSV activity was first observed in mid-late August in regional centers before emergence in the metropolitan area, with transmission potentially facilitated by increased travel within the state [7]. Conversely, the initial rise in RSV cases in WA preceded the opening of interstate borders, suggesting this pathway was not the primary mechanism. Our findings raise concerns for RSV control in the Northern Hemisphere, where a shortened season was experienced last winter [8]. The eventual reduction of COVID-19–related public health measures may herald a significant rise in RSV [9]. Depending on the timing, the accompanying morbidity and mortality, especially in older adults [6], may overburden already strained healthcare systems. To delineate the relative contribution of an increasingly susceptible population and the reduction in border restrictions, further surveillance, transmission studies, and assessment of relatedness of RSV strains is progressing. Show more