Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Minireviews
    • JVI Classic Spotlights
    • Archive
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JVI
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Journal of Virology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Minireviews
    • JVI Classic Spotlights
    • Archive
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JVI
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Genetic Diversity and Evolution

Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi

Khuzwayo C. Jere, Chrispin Chaguza, Naor Bar-Zeev, Jenna Lowe, Chikondi Peno, Benjamin Kumwenda, Osamu Nakagomi, Jacqueline E. Tate, Umesh D. Parashar, Robert S. Heyderman, Neil French, Nigel A. Cunliffe, Miren Iturriza-Gomara
Tom Gallagher, Editor
Khuzwayo C. Jere
aInstitute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
bMalawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Khuzwayo C. Jere
Chrispin Chaguza
aInstitute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
bMalawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chrispin Chaguza
Naor Bar-Zeev
aInstitute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
bMalawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
cCentre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jenna Lowe
aInstitute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chikondi Peno
bMalawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Benjamin Kumwenda
bMalawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Osamu Nakagomi
aInstitute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
dGraduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jacqueline E. Tate
eEpidemiology Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Umesh D. Parashar
eEpidemiology Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert S. Heyderman
bMalawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
fDivision of Infection and Immunity, University College London, London, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Neil French
bMalawi-Liverpool-Wellcome Trust Clinical Research Programme/Department of Medical Laboratory Sciences, College of Medicine, University of Malawi, Blantyre, Malawi
cCentre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nigel A. Cunliffe
cCentre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Miren Iturriza-Gomara
cCentre for Global Vaccine Research, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
gNIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tom Gallagher
Loyola University Medical Center
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/JVI.01246-17
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • FIG 1
    • Open in new tab
    • Download powerpoint
    FIG 1

    Rotavirus strains, genetic constellations, and phylogenetic networks of G1P[8] rotaviruses detected in Malawian children at QECH from 1997 to 2015. (a) Schematic representation of the proportions of all genotypes detected in rotavirus-positive stool samples. The size of the circle is directly proportional to the frequency of detection of G and P genotypes. There were no rotavirus surveillance activities in 2010; hence, samples were not collected at this time. (b) Bayesian maximum clade credibility tree for concatenated whole-rotavirus-genome sequences illustrating the genetic constellation and reassortment patterns for 32 pre- and 18 postvaccine G1P[8] strains from Malawi as well as the prototype Wa and DS-1 strains for comparison. Genotype and genogroup assignments for each segment were based on nucleotide sequence identities, assigned by using RotaC. Genome segments that were assigned the same genotype are shown with the same color and genotype numbers. (C) Phylogenetic network of complete concatenated whole-genome sequences of G1P[8] rotavirus strains detected in Malawi from 1998 to 2014. Branches are drawn to scale, and splits in the network indicate reassortments. Network clusters are color-coded and named in accordance with their phylogenic lineages (L1 to L3) that correlated with the time of strain isolation before or after rotavirus vaccine introduction. Clusters L1 (green) and L2 (blue) contain prevaccine G1P[8] strains, whereas L3 (red) contains postvaccine strains. Network subclusters within each main cluster are shaded in blue (L1), red (L2), or orange (L3).

  • FIG 2
    • Open in new tab
    • Download powerpoint
    FIG 2

    Bayesian maximum clade credibility (MCC) time tree based on complete nucleotide sequences illustrating lineage replacement within the genome segments encoding structural proteins of the G1P[8] strains that circulated in Malawi from 1998 to 2014. With the exception of VP4 and VP7 genes that had L2 and L3 genes sharing close ancestry, the rest had three distinct G1P[8] lineages. L1, L2, and L3 represent lineages 1, 2, and 3, respectively.

  • FIG 3
    • Open in new tab
    • Download powerpoint
    FIG 3

    Bayesian MCC time tree based on complete nucleotide sequences of the structural proteins for G1P[8] strains from Malawi. Only DS-1-like genome segments for typical DS-1-like strains that were assigned G2P[4], G2P[6], G8P[4], G8P[6], and G12P[6] outer capsid genotypes from Malawi were included to calculate evolutionary dynamics for VP1- to VP4-, VP6-, and VP7-encoding genome segments for the atypical DS-1-like G1P[8] strains (L3 cluster).

  • FIG 4
    • Open in new tab
    • Download powerpoint
    FIG 4

    Time to the most recent common ancestor (tMRCA), evolutionary rates for each genome segment of Malawian G1P[8] strains, and comparative population dynamics of G1P[8] rotavirus strains circulating in Malawi, 1998 to 2014. (a) Evolutionary rates and tMRCAs for each genome segment of the atypical Malawian G1P[8] strains shown together with their 95% highest posterior density (HPD) intervals. (b) Absolute values for the means and ranges of evolutionary rates and tMRCA at 95% HPD intervals. (c) Phylogenies and relative genetic diversities estimated by using the Gaussian Markov random field (GMRF) model represent Bayesian Skygrid plots for VP1- to VP4-, VP6-, and NSP1- to NSP5-encoding genome segments. Lines in the GMRF plot represent the mean relative genetic diversity through time.

  • FIG 5
    • Open in new tab
    • Download powerpoint
    FIG 5

    Amino acid substitutions and structural conformation of the outer capsid glycoprotein of Malawian G1P[8] strains. (a) Complete VP7 sequences of representative pre- and postvaccine G1P[8] strains aligned to that of RV1 exhibiting amino acid substitutions that occurred within the variable regions (VR) and mapped antigenic regions (AR) over time. Lineage-defining amino acid amino acid substitutions are highlighted in green, blue, and yellow for the L1, L2, and L3 lineages, respectively. Pre- and postvaccine strains are shown with vertical green and red bars on the right, respectively. Strains belonging to the L1, L2, and L3 phylogenetic clusters are shown with green, blue, and red bars, respectively, on the right. (b) Perfect alignment of superimposed VP7 structures exhibiting few differences between RV1 and L1 to L3 strains. Antigenic regions A, B, and C are shown in white. L1 to L3 and RV1 strains are shown in yellow, green, blue, and red, respectively. (c to e) Surface visualization of VP7 from outside the virion on the 3-fold axis displaying amino acid differences when structures for L1 (c), L2 (d), and L3 (e) G1P[8] strains were superimposed on the structure of the outer capsid glycoprotein of RV1. Numbers correspond to the positions where mutations occurred.

Tables

  • Figures
  • Additional Files
  • TABLE 1

    Evolutionary selective forces and recombination in all 11 proteins of the Malawian G1P[8] rotavirus strainsa

    ProteindN/dS by SLACω (β/α) by FUBAR
    VP10.05022.22
    VP20.05382.67
    VP30.09652.47
    VP40.10523.15
    VP60.03104.66
    VP70.20336.01
    NSP10.22394.21
    NSP20.09205.62
    NSP30.08705.44
    NSP40.10977.10
    NSP50.10977.47
    • ↵a Shown are posterior distributions of synonymous (α) and nonsynonymous (β) substitution rates over sites as well as mean posterior probabilities for a ω (β/α) value of <1 at a site. The consensus selective force in all cases was purifying selection, and there was no recombination determined by GARD or SBP.

Additional Files

  • Figures
  • Tables
  • Supplemental material

    • Supplemental file 1 -

      Table S1 (Whole-genotype constellations of pre- and postvaccine Malawian G1P[8] strains and reference rotaviruses.)

      XLS, 72K

    • Supplemental file 2 -

      Fig. S1 (G1P[8] rotavirus strains characterized from stool samples collected from Malawian infants at QECH from 1997 to 2015.)

      Fig. S2 (Phylogenetic analysis of complete ORFs for individual 11 genome segments of Malawian G1P[8] strains compared to reference strains from elsewhere using the maximum-likelihood method.)

      Fig. S3. Bayesian maximum clade credibility (MCC) time tree based on complete nucleotide sequences illustrating lineage replacement within the genome segments encoding nonstructural proteins of the G1P[8] strains that circulated in Malawi from 1998 to 2014.) Fig. S4 (Bayesian MCC time tree based on complete nucleotide sequences of nonstructural proteins for G1P[8] strains from Malawi.)

      PDF, 3.9M

PreviousNext
Back to top
Download PDF
Citation Tools
Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi
Khuzwayo C. Jere, Chrispin Chaguza, Naor Bar-Zeev, Jenna Lowe, Chikondi Peno, Benjamin Kumwenda, Osamu Nakagomi, Jacqueline E. Tate, Umesh D. Parashar, Robert S. Heyderman, Neil French, Nigel A. Cunliffe, Miren Iturriza-Gomara for the VACSURV Consortium
Journal of Virology Jan 2018, 92 (3) e01246-17; DOI: 10.1128/JVI.01246-17

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Journal of Virology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi
(Your Name) has forwarded a page to you from Journal of Virology
(Your Name) thought you would be interested in this article in Journal of Virology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Emergence of Double- and Triple-Gene Reassortant G1P[8] Rotaviruses Possessing a DS-1-Like Backbone after Rotavirus Vaccine Introduction in Malawi
Khuzwayo C. Jere, Chrispin Chaguza, Naor Bar-Zeev, Jenna Lowe, Chikondi Peno, Benjamin Kumwenda, Osamu Nakagomi, Jacqueline E. Tate, Umesh D. Parashar, Robert S. Heyderman, Neil French, Nigel A. Cunliffe, Miren Iturriza-Gomara for the VACSURV Consortium
Journal of Virology Jan 2018, 92 (3) e01246-17; DOI: 10.1128/JVI.01246-17
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • RESULTS
    • DISCUSSION
    • MATERIALS AND METHODS
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

KEYWORDS

rotavirus
phylodynamics
genome reassortment
lineage turnover
whole-genome sequencing
Malawi

Related Articles

Cited By...

About

  • About JVI
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #Jvirology

@ASMicrobiology

       

 

JVI in collaboration with

American Society for Virology

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Print ISSN: 0022-538X; Online ISSN: 1098-5514