ARTICLE | doi:10.20944/preprints202303.0219.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2 pandemic; PCR positivity; Aleph Delta Omicron waves; Mumbai; India
Online: 13 March 2023 (06:31:08 CET)
Background: The SARS-CoV-2 laboratory PCR tests were generally reported only as binary positive or negative outcomes. Instead test positivity, these results contain a great deal of epidemiological information related to viral transmission patterns in populations. These transmission patterns during India’s SARS-CoV-2 viral waves remain largely undocumented. Methods: We analysed 2.7 million real-time polymerase chain reaction (PCR) testing records collected in Mumbai, a bellwether for other Indian cities. We used the inverse of cycle threshold (Ct) values to determine community-level viral load. We quantified wave-specific differences by age, sex and slum population density. Results: Overall PCR positivity was 3.4% during non-outbreak periods, rising to 23.2% and 42.8% during the Aleph (June-November 2020) and Omicron waves (January 2022), respectively, but only 9.9% during the Delta wave (March-June 2021). The community-level median Ct values fell and rose ~7-14 days prior to PCR positivity rates. Viral loads were 4-fold higher during the Delta and Omicron waves than during non-outbreak months. The Delta wave had high viral loads at older ages, in women and in areas of higher slum density. During the Omicron wave, differences in viral load by sex and for slum density had disappeared, but older adults continued to show higher viral load. Conclusions: Mumbai’s viral waves had markedly high viral loads representing an early signal of pandemic trajectory. Continue the vaccination in elderly Indians could reduce viral load in subsequent waves. Ct values are practicable monitoring tools.