The prevalence of SARS-CoV-2 infection and other public health outcomes during the BA.2/BA.2.12.1 surge, New York City, April-May 2022
Authors: Qasmieh Saba A , Robertson McKaylee M , Teasdale Chloe A , Kulkarni Sarah G , Jones Heidi , Larsen David A. , Dennehy John J. , McNairy Margaret , Borrell Luisa N. , Nash Denis 
Published: May 2022

AbstractBackgroundRoutine case surveillance data for SARS-CoV-2 are incomplete, unrepresentative, missing key variables of interest, and may be increasingly unreliable for both timely surge detection and understanding the burden of infection and access to treatment.MethodsWe conducted a cross-sectional survey of a representative sample of 1,030 New York City (NYC) adult residents ≥18 years on May 7-8, 2022, when BA.2.12.1 comprised 47% of reported cases per genomic surveillance. We estimated the prevalence of SARS-CoV-2 infection during the preceding 14-day period (April 23-May 8), weighted to represent the 2020 NYC adult population. Respondents were asked about SARS-CoV-2 testing (including at-home rapid antigen tests), testing outcomes, COVID-like symptoms, and contact with SARS-CoV-2 cases. Based on responses, we classified individuals into three mutually exclusive categories of SARS-CoV-2 infection according to a hierarchical case definition as follows: confirmed (positive test with a provider), probable (positive at home rapid test), and possible (COVID-like symptoms and close contact with a confirmed/probable case). SARS-CoV-2 prevalence estimates were age- and sex-adjusted to the 2020 US population. Individuals with SARS-CoV-2 were asked about awareness/use of antiviral medications. We triangulated survey-based prevalence estimates with NYC’s official SARS-CoV-2 metrics on cases, hospitalizations, and deaths, as well as SARS-CoV-2 concentrations in wastewater for the same time period.ResultsAn estimated 22.1% (95%CI 17.9%-26.2%) of respondents had SARS-CoV-2 infection during the two-week study period, corresponding to ∼1.5 million adults (95%CI 1.3-1.8 million). The official SARS-CoV-2 case count during the study period was 51,218. This 22.1% prevalence estimate included 11.4%, 6.5%, and 4.3% who met the confirmed, probable, and possible criteria of our case definition, respectively. Prevalence was estimated at 34.9% (95%CI 26.9%-42.8%) among individuals with co-morbidities, 14.9% (95% CI 11.0%-18.8%) among those 65+ years, and 18.9% (95%CI 10.2%-27.5%) among unvaccinated persons. Hybrid immunity (i.e., history of both vaccination and prior infection) was 66.2% (95%CI 55.7%-76.7%) among those with COVID and 46.3% (95%CI 40.2-52.2) among those without. Among individuals with COVID, 44.1% (95%CI 33.0%-55.1%) were aware of the antiviral nirmatrelvir/ritonavir (Paxlovid™), and 15.1% (95%CI 7.1%-23.1%) reported receiving it. Deaths and hospitalizations increased, but remained well below the levels of the BA.1 surge. SARS-CoV-2 virus concentrations in wastewater surveillance showed only a modest signal in comparison to that of the BA.1 surge.Conclusions and RelevanceThe true magnitude of NYC’s BA.2/BA.2.12.1 surge may have been vastly underestimated by routine SARS-CoV-2 case counts and wastewater surveillance. Hybrid immunity, bolstered by the recent BA.1 surge, likely limited the impact of the BA.2/BA.2.12.1 surge on severe outcomes. Representative surveys are needed as part of routine surveillance for timely surge detection, and to estimate the true burden of infection, hybrid immunity, and uptake of time-sensitive treatments among those most vulnerable to severe COVID.Short abstractChanges in testing practices and behaviors, including increasing at-home rapid testing and decreasing provider-based testing make it challenging to assess the true prevalence of SARS-CoV-2. We conducted a population-representative survey of adults in New York City to estimate the prevalence of SARS-CoV-2 infection during the BA.2./BA.2.12.1 surge in late April/early May 2022. We triangulated survey-based SARS-CoV-2 prevalence estimates with contemporaneous city-wide SARS-CoV-2 metrics on diagnosed cases, hospitalizations, deaths, and SARS-CoV-2 concentration in wastewater. Survey-based prevalence estimates were nearly 30 times higher than official case counts, and estimates of recently acquired hybrid immunity among those with active infection were high. We conclude that no single data source provides a complete or accurate assessment of the epidemiologic situation. Taken together, however, our results suggest that the magnitude of the BA.2/BA.2.12.1 surge was likely significantly underestimated, and high levels of hybrid immunity likely prevented a major surge in BA.2/BA.2.12.1-associated hospitalizations/deaths.