key: cord-1004062-s96b0s76 authors: Mesfin, Y.; Chen, D.; Bond, H.; Lam, V.; Cheung, J.; Wong, J.; Ali, S. T.; Lau, E.; Wu, P.; Leung, G.; Cowling, B. J. title: Epidemiology of infections with SARS-CoV-2 Omicron BA.2 variant in Hong Kong, January-March 2022 date: 2022-04-14 journal: nan DOI: 10.1101/2022.04.07.22273595 sha: 4b89d72bf8475895681d7ebb96ba6ebc4b23db10 doc_id: 1004062 cord_uid: s96b0s76 Hong Kong reported 12,631 confirmed COVID-19 cases and 213 deaths in the first two years of the pandemic but experienced a major wave predominantly of Omicron BA.2.2 in early 2022 with over 1.1 million reported SARS-CoV-2 infections and more than 7900 deaths. Our data indicated a shorter incubation period, serial interval, and generation time of infections with Omicron than other SARS-CoV-2 variants. Omicron BA.2.2 cases without a complete primary vaccination series appeared to face a similar fatality risk to those infected in earlier waves with the ancestral strain. 3 Several variants of concern of SARS-CoV-2 have caused large outbreaks of infection and substantial mortality following the emergence of the ancestral strain in early 2020. The Omicron variant is the most recent variant to have spread globally, since the first detections in Botswana and South Africa in November 2021 [1, 2] . Hong Kong sustained four small epidemic waves in 2020-2021 with 12,631 confirmed cases cumulatively (1.6 cases per 1000 population). Two vaccines became available in early 2021 including the mRNA vaccine BNT162b2 Hong Kong has implemented intensive public health and social measures in responses to the COVID-19 pandemic since early 2020 including test-and-trace, isolation of confirmed cases, quarantine of close contacts and inbound travelers in addition to strict travel and border restrictions, and community-wide social distancing measures [3] . These measures had been highly effective in suppressing four previous local outbreaks in 2020 and 2021 but were unable to prevent a large epidemic (wave 5). Since January 2022 a series of stringent social distancing measures have been reimposed in response to the surge of local infections after a lull of reported COVID-19 cases after the end of the fourth wave by May 2021 [4], including suspension of faceto-face classes for all schools from 14 January [5] and school closure for an early summer break . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted April 14, 2022 , mask mandate in outdoor public places, a ban on group gatherings with more than 2 persons in public places and gatherings at private places involving more than two households, and a suspension of dine-in services after 6pm starting from 10 February [4] . However, the local infections have still reached a record high in wave 5 with over 1.1 million cases officially reported and more than 7600 deaths reported up to date ( Figure 1B ) while there were in total 12,631 cases and 213 fatalities documented in the first four waves. The daily number of cases detected through RT-PCR and rapid antigen tests peaked on 4 March 2022 after rising exponentially for more than a month with a doubling time of 3.4 days ( Figure 1C ). The Omicron variant of SARS-CoV-2 was first detected in Hong Kong when a within-hotel transmission event of BA.1 was identified in two travelers in hotel quarantine in November 2021 [8] . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Table 1 ). Ninety five percent of patients infected with Omicron BA.1 and BA.2 were estimated to have developed symptoms within 7.7 days and 7.0 days after exposure, respectively (Supplementary Table 1 ). The gamma distribution had the best fit for BA.1 incubation period distribution. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted April 14, 2022 The SARS-CoV-2 Omicron BA.2 variant has caused more than 1.1 million confirmed cases in Hong Kong (mid-year population 7.4 million) within three months in early 2022, 100-fold higher than all the cases confirmed over four epidemic waves in the previous two years. Not every infection would become a laboratory-confirmed case for various reasons [12] . The peak in the epidemic in early March despite no major change in social distancing measures is likely indicative of a sufficient number of infections to create herd immunity, at least temporarily, with subsequent infections "overshooting" that threshold [13] . [16] and milder severity in South Africa [17, 18] and elsewhere [19] [20] [21] . However, we found a similar fatality risk for unvaccinated cases in the early part of our fifth wave compared to earlier waves, indicating that the intrinsic severity of BA.2 may not be much lower than the ancestral strain if at all. We found that cases in persons who had a complete primary series at age of 65-79 years or Table 2 ). In a separate study, we estimated very high vaccine effectiveness against severe disease in older adults ≥ 60 years of age who received either three doses of the inactivated vaccine CoronaVac or two doses of BNT162b2 [22] . For adults ≥ 60 years of age, the World Health Organization recommend that three doses of inactivated vaccine are needed [23] . Our estimates of the CFR might slightly overestimate the fatality risk of Omicron in Hong Kong given there was a lack of information on the type of virus variant for all individual cases and a small number of cases including deaths from clusters of Delta infections might have been included in the analysis. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted April 14, 2022 World Health Organization [Internet]. Statement on Omicron sublineage BA.2 World Health Organization. COVID-19 weekly epidemiological update, edition 80 Centre for Health Protection of Department of Health Government tightens social distancing measures in view of changes in epidemic situation The Government of the Hong Kong Special Administrative Region Suspension of face-to-face classes of primary schools, kindergartens and kindergarten-cum-child care centres until Chinese New Year [press release]. 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(which was not certified by peer review) The copyright holder for this preprint this version posted The authors thank Julie Au, Chloe Chui, Caitriona Murphy, Faith Ho, and Dillon Adam for technical support. BJC consults for AstraZeneca, Fosun Pharma, GSK, Moderna, Pfizer, Roche and Sanofi Pasteur.The authors report no other potential conflicts of interest.. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)