Abstract
Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases. Community outbreaks were caused by novel introductions rather than a resurgence of circulating strains. Thus, local outbreak prevention requires strong border control and community surveillance, especially during periods of less stringent social restriction. Non-adherence to prolonged preventative measures may explain sustained local transmission observed during wave four in late 2020 and early 2021. We also found that, due to a tight transmission bottleneck, transmission of low-frequency single nucleotide variants between hosts is rare.
Highlights
Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission
Among two of the earliest locally circulating lineages, time-scaled phylogenetic analysis estimated a median time to most recent common ancestor of 30-December-2019 (95% Highest Posterior Density Interval (HPD) 24-December2019 to 1-January-2020), indicating direct ancestry to cases circulating prior to the earliest recognised introductions (Fig. 2a)
Identified transmission pairs beta-binomial statistical framework[24] we estimated the number of virions required to initiate infection was between one and three (Fig. 4a and Supplementary Table 8). This is consistent with data from transmission pairs estimated in the United Kingdom and Austria as well as between cats, showing the SARS-CoV-2 transmission bottleneck may be universally small. These results suggest that intra-host single nucleotide variants, defined as variants detected with a minimum depth of 100 reads and minimum frequency >3% but not represented in the sample’s consensus genome, are rarely transmitted from donor to recipient host
Summary
Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Hong Kong (population 7.5 million) has been relatively successful in prevention and control of community SARS-CoV-2 transmission by non-pharmaceutical means, combining intermittent public health and social restrictions, mandatory isolation of cases and quarantine of close contacts in designated facilities[13,14], and increasingly stringent inbound travel regulations to suppress introductions (Fig. 1). We show that during waves two to four, 90% of the confirmed community-acquired SARS-CoV-2 cases in Hong Kong were the result of only three virus introductions (PANGO lineages[15] B.3, B.1.1.63, and B.1.36.27) out of a total of 170 introductions identified through genome sequencing.
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