TY - JOUR
T1 - Next generation sequencing of near-full length genome of norovirus GII.4 from Botswana
AU - Makhaola, Kgomotso
AU - Moyo, Sikhulile
AU - Kebaabetswe, Lemme P.
N1 - Funding Information:
Dr. Sikhulile Moyo was partially supported by Sub-Saharan African Network for TB/HIV Research Excellence ( SANTHE ), a DELTAS Africa Initiative [grant number DEL-15-006 ]. The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS)’s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa's Development Planning and Coordinating Agency ( NEPAD Agency) with funding from the Wellcome Trust [grant number 107752/Z/15/Z ] and the United Kingdom (U.K.) government.
Funding Information:
We would like to thank Tsotlhe Rose Ditlhako and Dorcas Maruapula from the Botswana Harvard HIV Partnership for assisting with the Oxford MinION technology protocol. We would also like to thank Wonderful Tatenda Choga, also from Botswana Harvard HIV Partnership for assisting with epitope mapping and 3D structure. This study was funded by the Botswana International University of Science and Technology through a research initiation grant (grant number: R00005) offered to Dr. Lemme P. Kebaabetswe. Dr. Sikhulile Moyo was partially supported by Sub-Saharan African Network for TB/HIV Research Excellence (SANTHE), a DELTAS Africa Initiative [grant number DEL-15-006]. The DELTAS Africa Initiative is an independent funding scheme of the African Academy of Sciences (AAS)?s Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa's Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust [grant number 107752/Z/15/Z] and the United Kingdom (U.K.) government.
Funding Information:
This study was funded by the Botswana International University of Science and Technology through a research initiation grant (grant number: R00005 ) offered to Dr. Lemme P. Kebaabetswe.
Publisher Copyright:
© 2021
PY - 2021/9
Y1 - 2021/9
N2 - Noroviruses are highly diverse, with genotype GII.4 causing most epidemics. This study aimed to investigate the evolutionary dynamics of norovirus genogroup GII strains among acutely infected children under 5 years in Botswana, between 2016 and 2018. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to amplify the whole norovirus genome, followed by next-generation sequencing using Oxford Nanopore technology. Twelve samples were successfully analyzed, with 11 identified as norovirus GII.4 Sydney [P31] and one as GII.4 Sydney [P13]. This study generated the first near-full length norovirus sequences in Botswana (93–95% coverage). Our results show that the norovirus GII.4 strains circulating in Botswana are under evolution through recombination and antigenic drift. Recombination in the GII.4 Sydney [P31] and GII.4 Sydney [P13] strains occurred in the ORF1/ORF2 junction and within ORF1, respectively. This study provides the first description of the GII.4 Sydney [P13] recombinant. Amino acid variation in the immunogenic sites was analyzed. Mutations in epitope A correlate with the emergence of novel norovirus GII.4 strains with altered antigenicity. In this study, we identified 43 unique amino acid substitutions in the VP1 region, with six occurring in epitopes, A (G295N, and E368Q) and E (S40T, N412D, N412K and T413H). The shell subdomain of the GII.4 Sydney [P13] variant was closely related to norovirus GII.17. Lastly, we also observed several mutations in the T cell restricted epitopes of both strains. Our study has made a novel contribution to understanding the evolution of norovirus GII.4 in Botswana.
AB - Noroviruses are highly diverse, with genotype GII.4 causing most epidemics. This study aimed to investigate the evolutionary dynamics of norovirus genogroup GII strains among acutely infected children under 5 years in Botswana, between 2016 and 2018. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to amplify the whole norovirus genome, followed by next-generation sequencing using Oxford Nanopore technology. Twelve samples were successfully analyzed, with 11 identified as norovirus GII.4 Sydney [P31] and one as GII.4 Sydney [P13]. This study generated the first near-full length norovirus sequences in Botswana (93–95% coverage). Our results show that the norovirus GII.4 strains circulating in Botswana are under evolution through recombination and antigenic drift. Recombination in the GII.4 Sydney [P31] and GII.4 Sydney [P13] strains occurred in the ORF1/ORF2 junction and within ORF1, respectively. This study provides the first description of the GII.4 Sydney [P13] recombinant. Amino acid variation in the immunogenic sites was analyzed. Mutations in epitope A correlate with the emergence of novel norovirus GII.4 strains with altered antigenicity. In this study, we identified 43 unique amino acid substitutions in the VP1 region, with six occurring in epitopes, A (G295N, and E368Q) and E (S40T, N412D, N412K and T413H). The shell subdomain of the GII.4 Sydney [P13] variant was closely related to norovirus GII.17. Lastly, we also observed several mutations in the T cell restricted epitopes of both strains. Our study has made a novel contribution to understanding the evolution of norovirus GII.4 in Botswana.
UR - http://www.scopus.com/inward/record.url?scp=85108835597&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85108835597&partnerID=8YFLogxK
U2 - 10.1016/j.virusres.2021.198491
DO - 10.1016/j.virusres.2021.198491
M3 - Article
C2 - 34147552
AN - SCOPUS:85108835597
SN - 0168-1702
VL - 302
JO - Virus Research
JF - Virus Research
M1 - 198491
ER -
