2021
DOI: 10.1016/j.jhin.2021.02.022
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Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole-genome sequencing

Abstract: This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, a… Show more

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Cited by 33 publications
(44 citation statements)
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“…To overcome these short-read sequencing issues, there are two technologies carrying promise for studies of viral genome instability by generating long reads from individual polynucleotides, Oxford Nanopore Technology and Pacific Biosciences [ 147 ]. Each of the two platforms is plagued by a rather high sequencing error rate, but even with the current level of accuracy Oxford Nanopore was used for characterizing viromes [ 148 , 149 , 150 ]. Any further increase in sequencing accuracy may cause a revolution with viral genome instability research.…”
Section: Concluding Remarks and Future Questionsmentioning
confidence: 99%
“…To overcome these short-read sequencing issues, there are two technologies carrying promise for studies of viral genome instability by generating long reads from individual polynucleotides, Oxford Nanopore Technology and Pacific Biosciences [ 147 ]. Each of the two platforms is plagued by a rather high sequencing error rate, but even with the current level of accuracy Oxford Nanopore was used for characterizing viromes [ 148 , 149 , 150 ]. Any further increase in sequencing accuracy may cause a revolution with viral genome instability research.…”
Section: Concluding Remarks and Future Questionsmentioning
confidence: 99%
“…Novel single nucleotide polymorphism (SNP) (also known as sample-unique variants) was defined as specific nucleotide substitution in viral genome present in the corresponding sample only. A similar approach has been used to determine intra-hospital transmission of SARS-CoV-2 [ 2 , 5 ]. Multiple sequence alignment for consensus genomes was performed by Clustal Omega 1.2.0 ( http://www.clustal.org/omega/ ).…”
Section: Methodsmentioning
confidence: 99%
“…The current wave of community outbreak of coronavirus disease 2019 (COVID-19) in Hong Kong at the time of writing commenced in November 2020 and the total number of symptomatic and asymptomatic infected cases was greater than in previous waves. When there are ongoing outbreaks of COVID-19, healthcare workers (HCWs) may acquire the disease from communities or through nosocomial transmission such as patient-to-HCW and HCW-to-HCW [ [1] , [2] , [3] ]. To differentiate between community-acquired infection from hospital-acquired infection in HCWs, traditional epidemiological study alone may be inadequate [ 2 ].…”
Section: Introductionmentioning
confidence: 99%
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