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Genetic characterization of G12P6 and G12P8 rotavirus strains collected in six African countries between 2010 and 2014
Duncan Steele
Bill and Melinda Gates Foundation
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4946-037X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Infectious Diseases.
Background: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.
Methods: The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.
Results: The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related , irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 x10−3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.
Conclusions: At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.
Keywords
Rotavirus strains, Africa, G12, P[8], P[4]
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Editor invited
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Editorial decision: Major revision
On 30 Aug, 2020
Review #2 received
Received 28 Aug, 2020
Review #1 received
Received 24 Aug, 2020
Reviewer #1 agreed
On 21 Aug, 2020
Reviewer #2 agreed
On 21 Aug, 2020
Reviewers invited
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Editor assigned
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This preprint is under consideration at BMC Infectious Diseases. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Genetic characterization of G12P6 and G12P8 rotavirus strains collected in six African countries between 2010 and 2014
Duncan Steele
Bill and Melinda Gates Foundation
Corresponding Author
ORCiD: https://orcid.org/0000-0002-4946-037X
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Published
On 22 Jan, 2021
No community comments so far
Editorial decision: Accept
On 26 Dec, 2020
Editor assigned
On 24 Dec, 2020
Submission checks complete
On 24 Dec, 2020
Editor invited
On 24 Dec, 2020
Version 3
Posted 16 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 13 Dec, 2020
Editor assigned
On 02 Dec, 2020
Submission checks complete
On 02 Dec, 2020
Editor invited
On 02 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 07 Nov, 2020
Review #1 received
Received 05 Nov, 2020
Review #2 received
Received 01 Nov, 2020
Reviewer #2 agreed
On 30 Oct, 2020
Reviewers invited
Invitations sent on 29 Oct, 2020
Reviewer #1 agreed
On 29 Oct, 2020
Editor assigned
On 26 Oct, 2020
Submission checks complete
On 25 Oct, 2020
Editor invited
On 25 Oct, 2020
No comments provided
Editorial decision: Major revision
On 30 Aug, 2020
Review #2 received
Received 28 Aug, 2020
Review #1 received
Received 24 Aug, 2020
Reviewer #1 agreed
On 21 Aug, 2020
Reviewer #2 agreed
On 21 Aug, 2020
Reviewers invited
Invitations sent on 13 Aug, 2020
Editor assigned
On 05 Aug, 2020
Submission checks complete
On 04 Aug, 2020
Editor invited
On 04 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Infectious Diseases
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Infectious Diseases.
Background: G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.
Methods: The investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.
Results: The findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related , irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 x10−3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.
Conclusions: At present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.
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