The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 Surveillance How concurrent epidemics may introduce bias and decrease the observed SARS-CoV-2 percent positivity.

Background Circulation of seasonal non-SARS-CoV-2 respiratory viruses with syndromic overlap during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Methods Using a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory virus, we assess how an outbreak of secondary virus may affect two COVID-19 surveillance indicators: testing demand and positivity. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can help correct of the observed SARS-CoV-2 percent positivity and improve surveillance quality. Results We find that a non-SARS-CoV-2 epidemic strongly increases SARS-CoV-2 daily testing demand and artificially reduces the observed SARS-CoV-2 percent positivity for the duration of the outbreak. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positivity. Conclusions This study highlights that co-circulating respiratory viruses can distort SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR tests, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.