SARS-CoV-2 whole-genome sequencing Netherlands
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB48419 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR7222315_filtered.vcf.gz | Vcf | |||
| ERR7222315_consensus.fasta.gz | Fasta.gz | |||
| ERR7222315_output.tar.gz | Other | |||
| ERR7222300_output.tar.gz | Other | |||
| ERR7222300_consensus.fasta.gz | Fasta.gz |
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Project description:As the world is struggling to control the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), there is an urgency to develop effective control measures. Essential information is encoded in the virus genome sequence with accurate and complete SARS-CoV-2 sequences essential for tracking the movement and evolution of the virus and for guiding efforts to develop vaccines and antiviral drugs. While there is unprecedented SARS-CoV-2 sequencing efforts globally, approximately 19 to 43 per cent of the genomes generated monthly are gapped, reducing their information content. The current study documents the genome gap frequencies and their positions in the currently available data and provides an alternative primer set and a sequencing scheme to help improve the quality and coverage of the genomes.
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Project description:We developed an extraction-free qPCR assay to identify Omicron BA.1 cases and verified lineage by sequencing. We find that BA.2 variants show almost twice the viral load (Ct) compared to both BA.1 as well as Delta variants.
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Project description:Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.
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Project description:AimTo investigate the sources of infection among healthcare workers (HCWs) and patients in a teaching hospital in the Netherlands during the early stages of the coronavirus disease 2019 (COVID-19) pandemic using epidemiological and whole-genome sequencing data.MethodsFrom 3rd April to 11th May 2020, 88 HCWs and 215 patients were diagnosed with COVID-19. Whole-genome sequences were obtained for 30 HCWs and 20 patients.ResultsSeven and 11 sequence types were identified in HCWs and patients, respectively. Cluster A was the most common sequence type, detected in 23 (77%) HCWs; of these, 14 (61%) had direct patient contact and nine (39%) had indirect patient contact. In addition, seven patients who were not hospitalized in the COVID-19 cohort isolation ward who became positive during their admission were infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) cluster A. Following universal masking of all HCWs and emphasis on physical distancing during meals and breaks, no further evidence was found for patient-to-HCW or HCW-to-HCW transmission or vice versa.ConclusionThe finding that patients and HCWs were infected with SARS-CoV-2 cluster A suggests both HCW-to-HCW and HCW-to-patient transmission.
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Project description:BackgroundDuring the SARS-CoV-2 pandemic, healthcare workers (HCWs) are being exposed to infection both at work and in their communities. Determining where HCWs might have been infected is challenging based on epidemiological data alone. At Akershus University Hospital, Norway, several clusters of possible intra-hospital SARS-CoV-2 transmission were identified based on routine contact tracing.AimTo determine whether clusters of suspected intra-hospital SARS-CoV-2 transmission could be resolved by combining whole genome sequencing (WGS) of SARS-CoV-2 with contact tracing data.MethodsEpidemiological data were collected during routine contact tracing of polymerase chain reaction-confirmed SARS-CoV-2-positive HCWs. Possible outbreaks were identified as wards with two or more infected HCWs defined as close contacts who tested positive for SARS-CoV-2 less than three weeks apart. Viral RNA from naso-/oropharyngeal samples underwent nanopore sequencing in direct compliance to the ARTIC Network protocol.FindingsFive outbreaks were suspected from contact tracing. Viral consensus sequences from 24 HCWs, two patients, and seven anonymous samples were analysed. Two outbreaks were confirmed, one refuted, and two remained undetermined. One new potential outbreak was discovered.ConclusionCombined with epidemiological data, nanopore WGS was a useful tool for investigating intra-hospital SARS-CoV-2 transmission. WGS helped to resolve questions about possible outbreaks and to guide local infection prevention and control measures.
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Project description:Whole genome sequencing provides rapid insight into key information about the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), such as virus typing and key mutation site, and this information is important for precise prevention, control and tracing of coronavirus disease 2019 (COVID-19) outbreak in conjunction with the epidemiological information of the case. Nanopore sequencing is widely used around the world for its short sample-to-result time, simple experimental operation and long sequencing reads. However, because nanopore sequencing is a relatively new sequencing technology, many researchers still have doubts about its accuracy. The combination of the newly launched nanopore sequencing Q20+ kit (LSK112) and flow cell R10.4 is a qualitative improvement over the accuracy of the previous kits. In this study, we firstly used LSK112 kit with flow cell R10.4 to sequence the SARS-CoV-2 whole genome, and summarized the sequencing results of the combination of LSK112 kit and flow cell R10.4 for the 1200bp amplicons of SARS-CoV-2. We found that the proportion of sequences with an accuracy of more than 99% reached 30.1%, and the average sequence accuracy reached 98.34%, while the results of the original combination of LSK109 kit and flow cell R9.4.1 were 0.61% and 96.52%, respectively. The mutation site analysis showed that it was completely consistent with the final consensus sequence of next generation sequencing (NGS). The results showed that the combination of LSK112 kit and flow cell R10.4 allowed rapid whole-genome sequencing of SARS-CoV-2 without the need for verification of NGS.
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