Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination.

Proceedings of the National Academy of Sciences of the United States of America
Juliana CudiniJudith Breuer

Abstract

Recent sequencing efforts have led to estimates of human cytomegalovirus (HCMV) genome-wide intrahost diversity that rival those of persistent RNA viruses [Renzette N, Bhattacharjee B, Jensen JD, Gibson L, Kowalik TF (2011) PLoS Pathog 7:e1001344]. Here, we deep sequence HCMV genomes recovered from single and longitudinally collected blood samples from immunocompromised children to show that the observations of high within-host HCMV nucleotide diversity are explained by the frequent occurrence of mixed infections caused by genetically distant strains. To confirm this finding, we reconstructed within-host viral haplotypes from short-read sequence data. We verify that within-host HCMV nucleotide diversity in unmixed infections is no greater than that of other DNA viruses analyzed by the same sequencing and bioinformatic methods and considerably less than that of human immunodeficiency and hepatitis C viruses. By resolving individual viral haplotypes within patients, we reconstruct the timing, likely origins, and natural history of superinfecting strains. We uncover evidence for within-host recombination between genetically distinct HCMV strains, observing the loss of the parental virus containing the nonrecombinant fragment. The ...Continue Reading

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Citations

Nov 2, 2019·Nature Reviews. Immunology·Richard BerryJamie Rossjohn
May 10, 2020·PLoS Pathogens·Alessandra MozziManuela Sironi
Sep 29, 2020·Nature Communications·Marius Walter, Eric Verdin
Jun 9, 2020·Annual Review of Virology·Adam S Lauring
Dec 19, 2019·Scientific Reports·Patrizia CaposioKlaus Früh
Jun 28, 2019·Frontiers in Immunology·A Raj Kumar Patro
Dec 26, 2019·Proceedings of the National Academy of Sciences of the United States of America·Charlotte J HouldcroftJudith Breuer
Mar 7, 2020·The Journal of Infectious Diseases·Nazia Kabani, Shannon A Ross
Jul 3, 2020·Frontiers in Cellular and Infection Microbiology·Nicolás M SuárezAndrew J Davison
Dec 26, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey D Jensen, Timothy F Kowalik
Jul 17, 2020·Frontiers in Cellular and Infection Microbiology·Charlotte J HouldcroftMark R Wills
Nov 5, 2020·PLoS Pathogens·Maoz GelbartAdi Stern
Jan 29, 2021·Virus Evolution·Salvatore CamioloAndrew J Davison
Feb 27, 2021·Scientific Reports·Sina RüegerUNKNOWN Swiss HIV Cohort Study
Apr 30, 2020·Microorganisms·Rachele CaglianiManuela Sironi
May 4, 2021·Frontiers in Cellular and Infection Microbiology·Jasper GöttingTina Ganzenmueller
May 23, 2021·Briefings in Bioinformatics·Zhi-Luo DengAlice C McHardy
Jul 31, 2021·Frontiers in Microbiology·Benjamin MorgaJean-Baptiste Lamy
Aug 14, 2021·ELife·Gerry Tonkin-HillUNKNOWN Wellcome Sanger Institute COVID-19 Surveillance Team
Aug 26, 2021·British Journal of Haematology·Cristina VenturiniJudith Breuer
Sep 16, 2021·Journal of Virology·Wanxiaojie XiePhilip G Stevenson

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