Dataset Information

Genomic surveillance of COVID-19 cases in Beijing.

ABSTRACT: The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-frequency single nucleotide polymorphisms (SNPs). Genomic comparisons reveal higher genomic diversity in the imported group compared to both the Wuhan exposure and local transmission groups, indicating continuous genomic evolution during global transmission. The imported group show region-specific SNPs, while the intra-host single nucleotide variations present as random features, and show no significant differences among groups. Epidemiological data suggest that detection of cases at immigration with mandatory quarantine may be an effective way to prevent recurring outbreaks triggered by imported cases. Notably, we also identify a set of novel indels. Our data imply that SARS-CoV-2 genomes may have high mutational tolerance.

SUBMITTER: Du P

PROVIDER: S-EPMC7603498 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Genomic surveillance of COVID-19 cases in Beijing.

Du Pengcheng P Ding Nan N Li Jiarui J Zhang Fujie F Wang Qi Q Chen Zhihai Z Song Chuan C Han Kai K Xie Wen W Liu Jingyuan J Wang Linghang L Wei Lirong L Ma Shanfang S Hua Mingxi M Yu Fengting F Wang Lin L Wang Wei W An Kang K Chen Jianjun J Liu Haizhou H Gao Guiju G Wang Sa S Huang Yanyi Y Wu Angela R AR Wang Jianbin J Liu Di D Zeng Hui H Chen Chen C

Nature communications 20201030 1

The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-f ...[more]

PMID: 33127911

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Project description:BackgroundThe burden and influence of health-care associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is unknown. We aimed to examine the use of rapid SARS-CoV-2 sequencing combined with detailed epidemiological analysis to investigate health-care associated SARS-CoV-2 infections and inform infection control measures.MethodsIn this prospective surveillance study, we set up rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples collected from our hospital (Cambridge, UK) and a random selection from hospitals in the East of England, enabling sample-to-sequence in less than 24 h. We established a weekly review and reporting system with integration of genomic and epidemiological data to investigate suspected health-care associated COVID-19 cases.FindingsBetween March 13 and April 24, 2020, we collected clinical data and samples from 5613 patients with COVID-19 from across the East of England. We sequenced 1000 samples producing 747 high-quality genomes. We combined epidemiological and genomic analysis of the 299 patients from our hospital and identified 35 clusters of identical viruses involving 159 patients. 92 (58%) of 159 patients had strong epidemiological links and 32 (20%) patients had plausible epidemiological links. These results were fed back to clinical, infection control, and hospital management teams, leading to infection-control interventions and informing patient safety reporting.InterpretationWe established real-time genomic surveillance of SARS-CoV-2 in a UK hospital and showed the benefit of combined genomic and epidemiological analysis for the investigation of health-care associated COVID-19. This approach enabled us to detect cryptic transmission events and identify opportunities to target infection-control interventions to further reduce health-care associated infections. Our findings have important implications for national public health policy as they enable rapid tracking and investigation of infections in hospital and community settings.FundingCOVID-19 Genomics UK funded by the Department of Health and Social Care, UK Research and Innovation, and the Wellcome Sanger Institute.

Project description:ObjectivesThe aim of the study was to evaluate completeness and timeliness of the rapidly developed surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in England using patient-level data.Study designThis is an observational study wherein public health surveillance systems are evaluated.MethodsData were collected in the Public Health England's Second-Generation Surveillance System through routine laboratory reporting processes, as well as via enhanced testing in collaboration with commercial partners. Three periods were chosen to present developments in disease surveillance around the first pandemic wave in England. Completeness of valid entries for key demographic and epidemiological fields was summarised. Timeliness was assessed using recorded date intervals: from sample collection to the laboratory reporting a positive result, the positive result being received by the national surveillance system and the data being available for epidemiological analysis.ResultsIn each period, demographic variables were more than 95% complete and enhanced ethnicity more than 85%, allowing a rich understanding of the general characteristics of COVID-19 cases in England. The proportion of cases completing all reporting stages of the national system within 3 days of when the specimen was taken increased from 69.1% in period 1 to 76.6% in period 3. In period 3, the median number of days to complete all reporting stages decreased to 2, from 3 in previous periods. Analysis of each reporting stage offers suggestive evidence that timeliness of the system has improved as reporting has become established over time.ConclusionsTimely processing of data for epidemiological use was consistent and rapid once received by the national system. Delays in timeliness were most likely to occur in the first stage of the reporting process, before laboratory input to the surveillance platform. Existing national surveillance mechanisms enhanced during the response have succeeded in providing rapid collection and reporting of case data to facilitate epidemiological monitoring and analysis and guide public health policy and strategy.

Dataset Information

Genomic surveillance of COVID-19 cases in Beijing.

Publications

Genomic surveillance of COVID-19 cases in Beijing.

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