Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong

Abstract

After keeping infections at bay for two years, Hong Kong experienced a surge of Omicron BA.2 infections in early 2022 that overwhelmed the health care system, isolation facilities, and contact tracing capacity, leading to one of the highest per-capita death rates of COVID-19 in early 2022. The outbreak occurred against a backdrop of a dense population with low immunity towards natural SARS-CoV-2 infection, high vaccine hesitancy in vulnerable populations, comprehensive disease surveillance and the capacity for stringent public health and social measures. Using genome sequences and epidemiological data from this time, we reconstruct the epidemic trajectory of the BA.2 wave, estimate transmission and incidence rates, and evaluate the effectiveness of policy changes. We identify an increase in the effective reproductive rate (Re) to 9.5 in mid-January 2022, which preceded real-time estimates of transmission (Rt), revealing that BA.2 community transmission was under-ascertained weeks before the epidemic appeared to surge in mid-February 2022. Due to this, public health measures were relaxed in early February (Spring Festival) while Re increased and remained > 1 throughout February. An independent estimation of point prevalence and incidence using phylodynamics also indicates extensive superspreading at this time, which likely contributed to the rapid expansion of the epidemic. This study demonstrates that relying on Rt estimation methods dependent on case reporting can misinform epidemic response planning, sometimes with substantial consequences. There is a need for future research and implementation of improved estimates of epidemic growth in near real-time that combine multiple disparate data sources to better inform outbreak response policy.

Prevalence and risk factors of long COVID 6–12 months after infection with the Omicron variant among nonhospitalized patients in Hong Kong

“…The prevalence of long COVID in this study was similar to a systematic review (45%) that included over 0.7 million patients from different countries and infected by different variants of concern (wild‐type, Alpha, and Beta), 3 but lower than a study from China, where the prevalence of long COVID infected by various variants (wild‐type, Alpha, Beta, Delta, and Omicron) among mostly hospitalized patients was 90.4% 26 . The SARS‐CoV‐2 subvariants were not detected for patients in our study, the majority of COVID‐19 cases in the fifth wave of the Hong Kong outbreak were caused by Omicron BA.2 and related sublineages, the largest monophyletic lineage was BA.2.2, and only with limited detection of Omicron BA.1 and related sublineages and Delta AY.127 12 . A systematic review indicated that the prevalence of Omicron‐induced long COVID in 3 months (28.4%) was lower than other strains (wild‐type: 52.1%, Alpha: 65.8%, Delta: 34.6%) 27 .…”

“…26 The SARS-CoV-2 subvariants were not detected for patients in our study, the majority of COVID-19 cases in the fifth wave of the Hong Kong outbreak were caused by Omicron BA.2 and related sublineages, the largest monophyletic lineage was BA.2.2, and only with limited detection of Omicron BA.1 and related sublineages and Delta AY.127. 12 A systematic review indicated that the prevalence of Omicron-induced long COVID in 3 months (28.4%) was lower than other strains (wild-type: 52.1%, Alpha: 65.8%, Delta:…”

“…The Omicron dominated the fifth wave of the outbreak in Hong Kong has resulted in over 2.8 million confirmed cases and 13 120 death from December 2021 to January 2023 11 . According to genome sequencing during the Hong Kong's fifth wave, most COVID‐19 cases were caused by Omicron BA.2 (84.6%), only a small number of cases were caused by other sublineages, including Omicron BA.1 (11.5%) and Delta AY.127 (3.8%) 12 …”

“…11 According to genome sequencing during the Hong Kong's fifth wave, most COVID-19 cases were caused by Omicron BA.2 (84.6%), only a small number of cases were caused by other sublineages, including Omicron BA.1 (11.5%) and Delta AY.127 (3.8%). 12 Preliminary reports suggested that Omicron may cause less severe illness than Delta variant. 13 Moreover, an observational study conducted in the United Kingdom found lower odds of having COVID symptoms over 4 weeks following Omicron infection compare to Delta in adult populations.…”

Risk of within-hotel transmission of SARS-CoV-2 during on-arrival quarantine in Hong Kong: an epidemiological and phylogenomic investigation

“…Similarly, Hong Kong's fifth and largest COVID-19 wave was triggered by separate HQ transmissions of BA.2 outside the study period. 33 This wave comprised more than 1.1 million cases and over 9000 deaths, 34 demonstrating the potentially severe consequences of low-frequency HQ transmission events. Additionally, there have been other introductions of novel lineages in Hong Kong where the source could not be identified despite strict quarantine measures, including the unidentified introduction(s) which resulted in the third epidemic wave in Hong Kong.…”