Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak

Summary: Background: A characteristic feature of SARS-CoV-2 is its ability to transmit from pre- or asymptomatic patients, complicating the tracing of infection pathways and causing outbreaks. Despite several reports that whole genome sequencing (WGS) and haplotype networks are useful for epidemiol...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Fumihiro Ishikawa, Yuko Udaka, Hideto Oyamada, Keiko Ishino, Issei Tokimatsu, Hironori Sagara, Yuji Kiuchi
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Epidemiological analysis Haplotype networks Phylogenetic tree analysis Severe acute respiratory syndrome coronavirus 2 Whole genome sequencing Infectious and parasitic diseases RC109-216 Public aspects of medicine RA1-1270
Acceso en línea:	https://doaj.org/article/03d8f2bc2b394143ab8a5cd81732d103
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:03d8f2bc2b394143ab8a5cd81732d103
record_format	dspace
spelling	oai:doaj.org-article:03d8f2bc2b394143ab8a5cd81732d1032021-12-04T04:35:46ZGenetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak2590-088910.1016/j.infpip.2021.100190https://doaj.org/article/03d8f2bc2b394143ab8a5cd81732d1032021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2590088921000792https://doaj.org/toc/2590-0889Summary: Background: A characteristic feature of SARS-CoV-2 is its ability to transmit from pre- or asymptomatic patients, complicating the tracing of infection pathways and causing outbreaks. Despite several reports that whole genome sequencing (WGS) and haplotype networks are useful for epidemiologic analysis, little is known about their use in nosocomial infections. Aim: We aimed to demonstrate the advantages of genetic epidemiology in identifying the link in nosocomial infection by comparing single nucleotide variations (SNVs) of isolates from patients associated with an outbreak in Showa University Hospital. Methods: We used specimens from 32 patients in whom COVID-19 had been diagnosed using clinical reverse transcription-polymerase chain reaction tests. RNA of SARS-CoV-2 from specimens was reverse-transcribed and analysed using WGS. SNVs were extracted and used for lineage determination, phylogenetic tree analysis, and median-joining analysis. Findings: The lineage of SARS-CoV-2 that was associated with outbreak in Showa University Hospital was B.1.1.214, which was consistent with that found in the Kanto metropolitan area during the same period. Consistent with canonical epidemiological observations, haplotype network analysis was successful for the classification of patients. Additionally, phylogenetic tree analysis revealed three independent introductions of the virus into the hospital during the outbreak. Further, median-joining analysis indicated that four patients were directly infected by any of the others in the same cluster. Conclusion: Genetic epidemiology with WGS and haplotype networks is useful for tracing transmission and optimizing prevention strategies in nosocomial outbreaks.Fumihiro IshikawaYuko UdakaHideto OyamadaKeiko IshinoIssei TokimatsuHironori SagaraYuji KiuchiElsevierarticleEpidemiological analysisHaplotype networksPhylogenetic tree analysisSevere acute respiratory syndrome coronavirus 2Whole genome sequencingInfectious and parasitic diseasesRC109-216Public aspects of medicineRA1-1270ENInfection Prevention in Practice, Vol 3, Iss 4, Pp 100190- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Epidemiological analysis Haplotype networks Phylogenetic tree analysis Severe acute respiratory syndrome coronavirus 2 Whole genome sequencing Infectious and parasitic diseases RC109-216 Public aspects of medicine RA1-1270
spellingShingle	Epidemiological analysis Haplotype networks Phylogenetic tree analysis Severe acute respiratory syndrome coronavirus 2 Whole genome sequencing Infectious and parasitic diseases RC109-216 Public aspects of medicine RA1-1270 Fumihiro Ishikawa Yuko Udaka Hideto Oyamada Keiko Ishino Issei Tokimatsu Hironori Sagara Yuji Kiuchi Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak
description	Summary: Background: A characteristic feature of SARS-CoV-2 is its ability to transmit from pre- or asymptomatic patients, complicating the tracing of infection pathways and causing outbreaks. Despite several reports that whole genome sequencing (WGS) and haplotype networks are useful for epidemiologic analysis, little is known about their use in nosocomial infections. Aim: We aimed to demonstrate the advantages of genetic epidemiology in identifying the link in nosocomial infection by comparing single nucleotide variations (SNVs) of isolates from patients associated with an outbreak in Showa University Hospital. Methods: We used specimens from 32 patients in whom COVID-19 had been diagnosed using clinical reverse transcription-polymerase chain reaction tests. RNA of SARS-CoV-2 from specimens was reverse-transcribed and analysed using WGS. SNVs were extracted and used for lineage determination, phylogenetic tree analysis, and median-joining analysis. Findings: The lineage of SARS-CoV-2 that was associated with outbreak in Showa University Hospital was B.1.1.214, which was consistent with that found in the Kanto metropolitan area during the same period. Consistent with canonical epidemiological observations, haplotype network analysis was successful for the classification of patients. Additionally, phylogenetic tree analysis revealed three independent introductions of the virus into the hospital during the outbreak. Further, median-joining analysis indicated that four patients were directly infected by any of the others in the same cluster. Conclusion: Genetic epidemiology with WGS and haplotype networks is useful for tracing transmission and optimizing prevention strategies in nosocomial outbreaks.
format	article
author	Fumihiro Ishikawa Yuko Udaka Hideto Oyamada Keiko Ishino Issei Tokimatsu Hironori Sagara Yuji Kiuchi
author_facet	Fumihiro Ishikawa Yuko Udaka Hideto Oyamada Keiko Ishino Issei Tokimatsu Hironori Sagara Yuji Kiuchi
author_sort	Fumihiro Ishikawa
title	Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak
title_short	Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak
title_full	Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak
title_fullStr	Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak
title_full_unstemmed	Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak
title_sort	genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of sars-cov-2 infection in nosocomial outbreak
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/03d8f2bc2b394143ab8a5cd81732d103
work_keys_str_mv	AT fumihiroishikawa geneticepidemiologyusingwholegenomesequencingandhaplotypenetworksrevealedthelinkageofsarscov2infectioninnosocomialoutbreak AT yukoudaka geneticepidemiologyusingwholegenomesequencingandhaplotypenetworksrevealedthelinkageofsarscov2infectioninnosocomialoutbreak AT hidetooyamada geneticepidemiologyusingwholegenomesequencingandhaplotypenetworksrevealedthelinkageofsarscov2infectioninnosocomialoutbreak AT keikoishino geneticepidemiologyusingwholegenomesequencingandhaplotypenetworksrevealedthelinkageofsarscov2infectioninnosocomialoutbreak AT isseitokimatsu geneticepidemiologyusingwholegenomesequencingandhaplotypenetworksrevealedthelinkageofsarscov2infectioninnosocomialoutbreak AT hironorisagara geneticepidemiologyusingwholegenomesequencingandhaplotypenetworksrevealedthelinkageofsarscov2infectioninnosocomialoutbreak AT yujikiuchi geneticepidemiologyusingwholegenomesequencingandhaplotypenetworksrevealedthelinkageofsarscov2infectioninnosocomialoutbreak
_version_	1718372891233353728

Genetic epidemiology using whole genome sequencing and haplotype networks revealed the linkage of SARS-CoV-2 infection in nosocomial outbreak

Ejemplares similares