Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada

Abstract The emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of...

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Autores principales:	Calvin P. Sjaarda, Nazneen Rustom, Gerald A. Evans, David Huang, Santiago Perez-Patrigeon, Melissa L. Hudson, Henry Wong, Zhengxin Sun, T. Hugh Guan, Muhammad Ayub, Claudio N. Soares, Robert I. Colautti, Prameet M. Sheth
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1bd04f33c0d34f66b665d63fb4c09e09
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spelling	oai:doaj.org-article:1bd04f33c0d34f66b665d63fb4c09e092021-12-02T13:30:34ZPhylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada10.1038/s41598-021-83355-12045-2322https://doaj.org/article/1bd04f33c0d34f66b665d63fb4c09e092021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83355-1https://doaj.org/toc/2045-2322Abstract The emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18–30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.Calvin P. SjaardaNazneen RustomGerald A. EvansDavid HuangSantiago Perez-PatrigeonMelissa L. HudsonHenry WongZhengxin SunT. Hugh GuanMuhammad AyubClaudio N. SoaresRobert I. ColauttiPrameet M. ShethNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Calvin P. Sjaarda Nazneen Rustom Gerald A. Evans David Huang Santiago Perez-Patrigeon Melissa L. Hudson Henry Wong Zhengxin Sun T. Hugh Guan Muhammad Ayub Claudio N. Soares Robert I. Colautti Prameet M. Sheth Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
description	Abstract The emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18–30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.
format	article
author	Calvin P. Sjaarda Nazneen Rustom Gerald A. Evans David Huang Santiago Perez-Patrigeon Melissa L. Hudson Henry Wong Zhengxin Sun T. Hugh Guan Muhammad Ayub Claudio N. Soares Robert I. Colautti Prameet M. Sheth
author_facet	Calvin P. Sjaarda Nazneen Rustom Gerald A. Evans David Huang Santiago Perez-Patrigeon Melissa L. Hudson Henry Wong Zhengxin Sun T. Hugh Guan Muhammad Ayub Claudio N. Soares Robert I. Colautti Prameet M. Sheth
author_sort	Calvin P. Sjaarda
title	Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
title_short	Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
title_full	Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
title_fullStr	Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
title_full_unstemmed	Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada
title_sort	phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage covid-19 patients in ontario, canada
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/1bd04f33c0d34f66b665d63fb4c09e09
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Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada

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