Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel.
Adolescent
Adult
Aged
Aged, 80 and over
Base Sequence
Basic Reproduction Number
/ statistics & numerical data
Betacoronavirus
/ genetics
COVID-19
Child
Child, Preschool
Communicable Diseases, Imported
/ epidemiology
Coronavirus Infections
/ epidemiology
Female
Genome, Viral
/ genetics
Humans
Infant
Infant, Newborn
Israel
/ epidemiology
Male
Middle Aged
Pandemics
/ prevention & control
Phylogeny
Pneumonia, Viral
/ epidemiology
Psychological Distance
RNA, Viral
/ genetics
SARS-CoV-2
Sequence Analysis, RNA
United States
Young Adult
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
02 11 2020
02 11 2020
Historique:
received:
12
06
2020
accepted:
02
10
2020
entrez:
3
11
2020
pubmed:
4
11
2020
medline:
18
11
2020
Statut:
epublish
Résumé
Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.
Identifiants
pubmed: 33139704
doi: 10.1038/s41467-020-19248-0
pii: 10.1038/s41467-020-19248-0
pmc: PMC7606475
doi:
Substances chimiques
RNA, Viral
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5518Références
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
PLoS Comput Biol. 2013;9(3):e1002947
pubmed: 23555203
Science. 2020 May 8;368(6491):638-642
pubmed: 32234804
Wellcome Open Res. 2020 Apr 9;5:67
pubmed: 32685698
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650
pubmed: 30958812
Lancet Infect Dis. 2020 Aug;20(8):911-919
pubmed: 32353347
Cell. 2020 Aug 20;182(4):812-827.e19
pubmed: 32697968
Nature. 2005 Nov 17;438(7066):355-9
pubmed: 16292310
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
PLoS Comput Biol. 2018 Nov 13;14(11):e1006546
pubmed: 30422979
Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):338-42
pubmed: 8990210
Cell. 2020 May 28;181(5):990-996.e5
pubmed: 32386545
Virus Res. 2014 Dec 19;194:191-9
pubmed: 25278144
Lancet. 2020 Feb 15;395(10223):497-506
pubmed: 31986264
Nat Microbiol. 2020 Jul;5(7):876-877
pubmed: 32427978
Nat Rev Genet. 2018 Jan;19(1):9-20
pubmed: 29129921
Science. 2020 Oct 30;370(6516):571-575
pubmed: 32913002
Genet Med. 2018 Jun;20(6):574-582
pubmed: 29240076
Science. 2020 Oct 30;370(6516):564-570
pubmed: 32912998
N Engl J Med. 2020 Feb 20;382(8):727-733
pubmed: 31978945
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
N Engl J Med. 2019 Dec 26;381(26):2569-2580
pubmed: 31881145
Science. 2020 May 22;368(6493):860-868
pubmed: 32291278
PLoS Pathog. 2019 Oct 31;15(10):e1008042
pubmed: 31671157
Mol Biol Evol. 2016 Oct;33(10):2735-43
pubmed: 27343287
J Virol. 2020 Jul 1;94(14):
pubmed: 32357959
Nat Med. 2020 May;26(5):672-675
pubmed: 32296168
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
pubmed: 9254694
BMC Bioinformatics. 2019 May 10;20(1):236
pubmed: 31077131
mBio. 2020 Jul 21;11(4):
pubmed: 32694143
Genetics. 2012 Jan;190(1):187-201
pubmed: 22042576