Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness.
Journal
Nature microbiology
ISSN: 2058-5276
Titre abrégé: Nat Microbiol
Pays: England
ID NLM: 101674869
Informations de publication
Date de publication:
05 2022
05 2022
Historique:
received:
06
08
2021
accepted:
15
03
2022
pubmed:
29
4
2022
medline:
6
5
2022
entrez:
28
4
2022
Statut:
ppublish
Résumé
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
Identifiants
pubmed: 35484231
doi: 10.1038/s41564-022-01105-z
pii: 10.1038/s41564-022-01105-z
pmc: PMC9084242
mid: NIHMS1789713
doi:
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
640-652Subventions
Organisme : NIAID NIH HHS
ID : R01 AI152703
Pays : United States
Organisme : NHLBI NIH HHS
ID : U54 HL143541
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI139246
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Cell Death Dis. 2020 Nov 6;11(11):957
pubmed: 33159040
PLoS Pathog. 2021 Aug 23;17(8):e1009849
pubmed: 34424945
Sci Signal. 2017 Dec 12;10(509):
pubmed: 29233916
Science. 2021 Jan 15;371(6526):
pubmed: 33234698
Elife. 2021 Feb 23;10:
pubmed: 33620317
Nat Commun. 2020 Oct 30;11(1):5493
pubmed: 33127906
Proc Natl Acad Sci U S A. 2021 Dec 7;118(49):
pubmed: 34857628
Lancet Infect Dis. 2020 Jun;20(6):697-706
pubmed: 32224310
Am J Epidemiol. 2006 Nov 15;164(10):936-44
pubmed: 16968863
Cell. 2020 May 28;181(5):1036-1045.e9
pubmed: 32416070
Sci Transl Med. 2021 Oct 27;13(617):eabh1803
pubmed: 34705523
J Virol. 2006 Aug;80(15):7590-9
pubmed: 16840338
PLoS Pathog. 2021 Apr 7;17(4):e1009499
pubmed: 33826681
Nat Commun. 2021 Jan 11;12(1):267
pubmed: 33431879
Science. 2021 Aug 6;373(6555):642-648
pubmed: 34168070
Nucleic Acids Res. 2008 Aug;36(14):e91
pubmed: 18603594
Nat Med. 2020 Aug;26(8):1200-1204
pubmed: 32555424
Nature. 2015 Oct 1;526(7571):122-5
pubmed: 26416728
Lancet Infect Dis. 2020 Aug;20(8):911-919
pubmed: 32353347
Emerg Infect Dis. 2020 Jul;26(7):1633-1635
pubmed: 32294051
Nat Med. 2020 Nov;26(11):1714-1719
pubmed: 32943787
Lancet Infect Dis. 2021 May;21(5):629-636
pubmed: 33545090
Front Microbiol. 2018 Jul 10;9:1554
pubmed: 30042759
J Toxicol Environ Health. 1997 Apr 11;50(5):475-506
pubmed: 9140466
Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7001-7003
pubmed: 32165541
Science. 2020 Jun 26;368(6498):1481-1486
pubmed: 32350060
Cell. 2020 Jul 23;182(2):429-446.e14
pubmed: 32526206
Nature. 2005 Nov 17;438(7066):355-9
pubmed: 16292310
Nature. 2020 May;581(7809):465-469
pubmed: 32235945
Nat Commun. 2021 Jan 12;12(1):323
pubmed: 33436609
PLoS Biol. 2021 Jul 12;19(7):e3001333
pubmed: 34252080
Nat Rev Immunol. 2013 Dec;13(12):875-87
pubmed: 24157572
Science. 2020 May 1;368(6490):489-493
pubmed: 32179701
Sci Adv. 2020 Nov 20;6(47):
pubmed: 33097472
Science. 2021 Apr 9;372(6538):
pubmed: 33658326
PLoS Comput Biol. 2012;8(6):e1002588
pubmed: 22761567
Proc Biol Sci. 2021 Feb 24;288(1945):20203002
pubmed: 33622135
Clin Infect Dis. 2021 Nov 2;73(9):e2861-e2866
pubmed: 33479756
Trends Microbiol. 2021 Oct;29(10):919-929
pubmed: 34059436
J Korean Med Sci. 2020 Feb 24;35(7):e86
pubmed: 32080991
J Infect Dis. 2021 Sep 17;224(6):976-982
pubmed: 34191025
Science. 2021 Jul 9;373(6551):
pubmed: 34035154
Int J Infect Dis. 2021 Apr;105:753-755
pubmed: 33684558
Clin Infect Dis. 2021 Aug 16;73(4):e860-e869
pubmed: 33104776
SIAM Rev Soc Ind Appl Math. 2011 Jan 1;53(1):3-39
pubmed: 21785515
J Dent Res. 1987 Aug;66(8):1300-2
pubmed: 3476596
Clin Pharmacol Ther. 2021 Apr;109(4):829-840
pubmed: 33410134
MMWR Morb Mortal Wkly Rep. 2020 Aug 07;69(31):1023-1025
pubmed: 32759921
N Engl J Med. 2021 Dec 23;385(26):2489-2491
pubmed: 34941024
JAMA. 2020 Apr 21;323(15):1488-1494
pubmed: 32125362
CPT Pharmacometrics Syst Pharmacol. 2020 Sep;9(9):509-514
pubmed: 32558354
Cell. 2021 May 13;184(10):2587-2594.e7
pubmed: 33861950
Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):
pubmed: 33536313
Nat Med. 2020 May;26(5):672-675
pubmed: 32296168
BMJ. 2020 Apr 21;369:m1443
pubmed: 32317267
Nat Commun. 2022 Jun 9;13(1):3207
pubmed: 35680861
Nat Commun. 2022 Jun 14;13(1):3416
pubmed: 35701424
Nature. 2021 May;593(7858):266-269
pubmed: 33767447
Lancet Infect Dis. 2021 Feb;21(2):165
pubmed: 32445709
PLoS Med. 2008 Mar 25;5(3):e74
pubmed: 18366252
EBioMedicine. 2021 Nov;73:103637
pubmed: 34678613
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Sci Adv. 2021 Jan 1;7(1):
pubmed: 33219112
Nat Med. 2021 May;27(5):892-903
pubmed: 33767405