South Asia's COVID-19 History and Surveillance: Updated Epidemiological Assessment

Background: This study updates our findings from the COVID-19 pandemic surveillance we first conducted in South Asia in2020 with 2 additional years of data for the region. We assess whether COVID-19 had transitioned from pandemic to endemicat the point the World Health Organization (WHO) ended the public health emergency status for COVID-19 on May 5, 2023. Objective: First, we aim to measure whether there was an expansion or contraction in the pandemic in South Asia around theWHO declaration. Second, we use dynamic and genomic surveillance methods to describe the history of the pandemic in theregion and situate the window of the WHO declaration within the broader history. Third, we aim to provide historical context forthe course of the pandemic in South Asia. Methods: In addition to updating the traditional surveillance data and dynamic panel estimates from our original study, thisstudy used data on sequenced SARS-CoV-2 variants from the Global Initiative on Sharing All Influenza Data (GISAID) to identifythe appearance and duration of variants of concern. We used Nextclade nomenclature to collect clade designations from sequencesand Pangolin nomenclature for lineage designations of SARS-CoV-2. Finally, we conducted a 1-sided ttest to determine whetherregional weekly speed or transmission rate per 100,000 population was greater than an outbreak threshold of 10. We ran the testiteratively with 6 months of data across the sample period. Results: Speed for the region had remained below the outbreak threshold for over a year by the time of the WHO declaration.Acceleration and jerk were also low and stable. While the 1-day persistence coefficients remained statistically significant andpositive (1.168), the 7-day persistence coefficient was negative (-0.185), suggesting limited cluster effects in which cases on agiven day predict cases 7 days forward. Furthermore, the shift parameters for either of the 2 most recent weeks around May 5,2023, did not indicate any overall change in the persistence measure around the time of the WHO declaration. From December of 2021 onward, Omicron was the predominant variant of concern in sequenced viral samples. The rolling ttest of speed equalto 10 was statistically insignificant across the entire pandemic. Conclusions: While COVID-19 continued to circulate in South Asia, the rate of transmission had remained below the outbreakthreshold for well over a year ahead of the WHO declaration. COVID-19 is endemic in the region and no longer reaches thethreshold of the pandemic definition. Both standard and enhanced surveillance metrics confirm that the pandemic had ended bythe time of the WHO declaration. Prevention policies should be a focus ahead of future pandemics. On that point, policy shouldemphasize an epidemiological task force with widespread testing and a contact-tracing system.