Navigating from SARS-CoV-2 elimination to endemicity in Australia, Hong Kong, New Zealand, and Singapore.
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ABSTRACT:
SUBMITTER: De Foo C
PROVIDER: S-EPMC8489883 | biostudies-literature | 2021 Oct
REPOSITORIES: biostudies-literature
Publications
Navigating from SARS-CoV-2 elimination to endemicity in Australia, Hong Kong, New Zealand, and Singapore.
De Foo Chuan C Grépin Karen A KA Cook Alex R AR Hsu Li Yang LY Bartos Michael M Singh Sudhvir S Asgari Nima N Teo Yik Ying YY Heymann David L DL Legido-Quigley Helena H
Lancet (London, England) 20211004 10311
Similar Datasets
Project description:Hong Kong utilized an elimination strategy with intermittent use of public health and social measures and increasingly stringent travel regulations to control SARS-CoV-2 transmission. By analyzing >1700 genome sequences representing 17% 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, two of which circulated cryptically for weeks while less stringent measures were in place. We found that SARS-CoV-2 within-host diversity was most similar among transmission pairs and epidemiological clusters due to a strong transmission bottleneck through which similar genetic background generates similar within-host diversity. Out of the 170 detected introductions of SARS-CoV-2 in Hong Kong during 2020, three introductions caused 90% of community cases.
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Project description: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.
| S-EPMC8825829 | biostudies-literature
Project description:BackgroundCOVID-19 pandemic has caused significant morbidity and mortality globally. As vaccines have been developed under expedited conditions, their safety and efficacy are being questioned by some populations leading to vaccine hesitancy, resulting in delayed vaccine uptake and herd immunity. This study aims to adopt a combination of Health Belief Model and other independent risk factors associated with high vaccine acceptance.MethodsAn anonymized cross-sectional survey was distributed between 15 January and 3 February 2021 across Singapore, Hong Kong and Australia among adult respondents through a certified online panel. Exploratory factor analysis and confirmatory factor analysis were carried out to assess perception constructs followed by multivariate regression modelling to assess factors associated with high vaccine acceptance against SARS_CoV-2.ResultsA total of 3,133 anonymised participants from Singapore (n = 1,009), Australia (n = 1,118) and Hong Kong (n = 1,006) completed the survey. While age and gender were not significantly associated, Asian ethnicity, current smokers and self-efficacy were significant associated factors of increased vaccine acceptance. While specific practices like taking micronutrients more frequently, cleaning and disinfecting their house more often were positively associated with increased vaccine acceptance, seeking medical help for COVID-19 symptoms like loss of smell/taste and overall COVID-19 knowledge score were negatively associated. Increased likelihood of vaccine acceptance was seen among those that obtained COVID-19 information less frequently and used digital media or non-health-related sources like influencers as a source of information. Among the eight perception constructs, perceived susceptibility and perceived response efficacy were positively associated, while perceived barriers were negatively associated with high vaccine acceptance.ConclusionWhile demographic parameters have weak association with vaccine acceptance, perceptions and practices parameters can help to better understand and influence vaccine acceptance. Study findings should provide guidance on the risk communication strategy to enhance vaccine acceptance for vaccination and boosters against new SARS-CoV-2 variants.
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Project description:IntroductionWith the economic recession and pandemic fatigue, milder viral variants and higher vaccine coverage along the time lay the basis for lifting anti-COVID policies to restore COVID-19 normalcy. However, when and how to adjust the anti-COVID policies remain under debate in many countries.MethodsIn this study, four countries (Singapore, South Korea, Australia, and New Zealand) and one region (Hong Kong SAR), that have shifted from the zero-COVID (ZC) policy to or close to the living-with-COVID (LWC) during or after the Omicron outbreak, were selected as research objects. All-cause mortality data were collected for these objects from 2009 to 2019. The expected mortality was estimated by a simple linear regression method. Excess mortality over time was calculated as the difference between the expected mortality and the observed mortality. Finally, percent excess mortality (PEM) was calculated as the excess mortality divided by the expected mortality.ResultsIn the examined four countries, PEM fluctuated around 0% and was lower than 10% most of the time under the ZC policy before 2022. After shifting to the LWC policy, all the examined countries increased the PEM. Briefly, countries with high population density (Singapore and South Korea) experienced an average PEM of 20-40% during the first half of 2022, and followed by a lower average PEM of 15-18% during the second half of 2022. For countries with low population density under the LWC policy, Australia experienced an average PEM of 39.85% during the first half of 2022, while New Zealand was the only country in our analysis that achieved no more than 10% in average PEM all the time. On the contrary, Hong Kong SAR under their ZC policy attained an average PEM of 71.14% during the first half of 2022, while its average PEM decreased to 9.19% in the second half of 2022 with LWC-like policy.ConclusionPEM under different policies within each country/region overtime demonstrated that the mortality burden caused by COVID-19 had been reduced overtime. Moreover, anti-COVID policies are suggested to control the excess mortality to achieve as low as 10% in PEM.
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Project description:We sequenced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from deep throat saliva samples of three imported cases in Hong Kong by Nanopore sequencing. Epidemiological and clinical features of these coronavirus disease 2019 (COVID-19) cases were presented for genomic epidemiology studies.
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Project description:BACKGROUND:The spike glycoprotein (S) gene of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) has been useful in analyzing the molecular epidemiology of the 2003 SARS outbreaks. OBJECTIVES:To characterize complete SARS-CoV S-gene sequences from Hong Kong. STUDY DESIGN:Fifty-six SARS-CoV S-gene sequences, obtained from patients who presented with SARS to the Prince of Wales Hospital during March-May 2003, were analysed using a maximum likelihood (ML) approach, together with 138 other (both human and animal) S-gene sequences downloaded from GenBank. RESULTS:The maximum-likelihood (ML) trees showed little evolution occurring within these 56 sequences. Analysis with the other sequences, showed three distinct SARS clusters, closely correlated to previously defined early, middle and late phases of the 2003 international SARS outbreaks. In addition, two new single nucleotide variations (SNVs), T21615A and T21901A, were discovered, not previously reported elsewhere. CONCLUSIONS:The ML approach to the reconstruction of tree phylogenies is known to be superior to the more popular, less computationally and time-demanding neighbour-joining (NJ) approach. The ML analysis in this study confirms the previously reported SARS epidemiology analysed mostly using the NJ approach. The two new SNVs reported here are most likely due to the tissue-culture passaging of the clinical samples.
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Project description:To investigate a superspreading event at a fitness center in Hong Kong, China, we used genomic sequencing to analyze 102 reverse transcription PCR-confirmed cases of severe acute respiratory syndrome coronavirus 2 infection. Our finding highlights the risk for virus transmission in confined spaces with poor ventilation and limited public health interventions.
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Project description:We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our results suggest that international or regional travel hubs might be useful surveillance sites to monitor sequence diversity.
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