SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia.

MBio
John EverettFrederic Bushman

Abstract

The severe acute respiratory coronavirus 2 (SARS-CoV-2) is the cause of the global outbreak of COVID-19. The epidemic accelerated in Philadelphia, PA, in the spring of 2020, with the city experiencing a first peak of infections on 15 April, followed by a decline through midsummer. Here, we investigate spread of the epidemic in the first wave in Philadelphia using full-genome sequencing of 52 SARS-CoV-2 samples obtained from 27 hospitalized patients collected between 30 March and 17 July 2020. Sequences most commonly resembled lineages circulating at earlier times in New York, suggesting transmission primarily from this location, though a minority of Philadelphia genomes matched sequences from other sites, suggesting additional introductions. Multiple genomes showed even closer matches to other Philadelphia isolates, suggestive of ongoing transmission within Philadelphia. We found that all of our isolates contained the D614G substitution in the viral spike and belong to lineages variously designated B.1, Nextstrain clade 20A or 20C, and GISAID clade G or GH. There were no viral sequence polymorphisms detectably associated with disease outcome. For some patients, genome sequences were determined longitudinally or concurrently fro...Continue Reading

References

Mar 6, 2008·Nature Reviews. Genetics·Siobain DuffyEdward C Holmes
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
May 24, 2018·Bioinformatics·James HadfieldRichard A Neher
Mar 18, 2020·The New England Journal of Medicine·Neeltje van DoremalenVincent J Munster
Apr 16, 2020·Environment International·Lidia Morawska, Junji Cao
May 21, 2020·Nature·Xiaonan ZhangHongzhou Lu
May 22, 2020·Nature·Hauke S HillenPatrick Cramer
May 31, 2020·Science·Ana S Gonzalez-ReicheHarm van Bakel
Jun 9, 2020·BioRxiv : the Preprint Server for Biology·Jennifer HarcourtNatalie J Thornburg
Jun 9, 2020·BioRxiv : the Preprint Server for Biology·Xiaojun LiFeng Gao
Jun 12, 2020·Proceedings of the National Academy of Sciences of the United States of America·Ayal B GussowEugene V Koonin
Jun 17, 2020·The Lancet Infectious Diseases·UNKNOWN WHO Working Group on the Clinical Characterisation and Management of COVID-19 infection
Jun 27, 2020·BioRxiv : the Preprint Server for Biology·Zharko DaniloskiNeville E Sanjana
Jun 27, 2020·BioRxiv : the Preprint Server for Biology·Lizhou ZhangHyeryun Choe
Jul 7, 2020·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Lidia Morawska, Donald K Milton
Jul 9, 2020·BioRxiv : the Preprint Server for Biology·Leonid YurkovetskiyJeremy Luban
Jul 10, 2020·Journal of Virology·Blanca TaboadaCarlos F Arias
Jul 11, 2020·Nature Structural & Molecular Biology·Antoni G WrobelSteven J Gamblin
Jul 11, 2020·JAMA : the Journal of the American Medical Association·W Joost WiersingaHallie C Prescott
Jul 17, 2020·Nature Microbiology·Andrew RambautOliver G Pybus
Jul 18, 2020·MedRxiv : the Preprint Server for Health Sciences·Gage Kahl MorenoThomas C Friedrich
Jul 18, 2020·Nature Medicine·Bas B Oude MunninkUNKNOWN Dutch-Covid-19 response team
Jul 25, 2020·Science·Darlan S CandidoNuno Rodrigues Faria
Sep 2, 2020·BioRxiv : the Preprint Server for Biology·Bryan A JohnsonVineet D Menachery
Sep 10, 2020·Proceedings of the National Academy of Sciences of the United States of America·Brian A Rabe, Constance Cepko

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Citations

Jun 10, 2021·European Journal of Medical Research·SeyedAhmad SeyedAlinaghi Shayesteh Jahanfar
Jul 3, 2021·Journal of Clinical Medicine·Thi Loi DaoPhilippe Gautret

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Datasets Mentioned

BETA
MW001232
MW001286

Methods Mentioned

BETA
GISAID
PCR
Illumina sequencing
reverse transcription-PCR
amplicon sequencing

Software Mentioned

Augur informatics
PERMANOVA
POLAR
bcftools
SAMtools
IQ
MAFFT
TREE

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