Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi

Chimwemwe Mhango; Akuzike Banda; End Chinyama; Jonathan J Mandolo; Orpha Kumwenda; Chikondi Malamba-Banda; Kayla G Barnes; Benjamin Kumwenda; Kondwani C Jambo; Celeste M Donato; Mathew D Esona; Peter N Mwangi; A Duncan Steele; Miren Iturriza-Gomara; Nigel A Cunliffe; Valentine N Ndze; Arox W Kamng'ona; Francis E Dennis; Martin M Nyaga; Chrispin Chaguza; Khuzwayo C Jere

doi:10.1093/ve/vead030

Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi

Virus Evol. 2023 May 22;9(1):vead030. doi: 10.1093/ve/vead030. eCollection 2023.

Authors

Chimwemwe Mhango^{1

2}, Akuzike Banda³, End Chinyama¹, Jonathan J Mandolo^{1

2}, Orpha Kumwenda¹, Chikondi Malamba-Banda^{1

4

5

6}, Kayla G Barnes¹, Benjamin Kumwenda², Kondwani C Jambo^{1

7}, Celeste M Donato^{8

9}, Mathew D Esona¹⁰, Peter N Mwangi¹¹, A Duncan Steele¹⁰, Miren Iturriza-Gomara¹², Nigel A Cunliffe^{4

13}, Valentine N Ndze¹⁴, Arox W Kamng'ona^{1

2}, Francis E Dennis¹⁵, Martin M Nyaga, Chrispin Chaguza^{4

16

17

18}, Khuzwayo C Jere^{1

4

6

13

11}

Affiliations

¹ Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi.
² Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi.
³ Department of Computer Science, Faculty of Science, University of Malawi, Zomba 305205, Malawi.
⁴ Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK.
⁵ Department of Biological Sciences, Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo 310105, Malawi.
⁶ Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre 312225, Malawi.
⁷ Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.
⁸ Enteric Diseases Group, Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Melbourne 3052, Australia.
⁹ Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia.
¹⁰ Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa.
¹¹ Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of Free State, Bloemfontein 9300, South Africa.
¹² Centre for Vaccine Innovation and Access, Program for Appropriate Technology in Health (PATH), Geneva 1218, Switzerland.
¹³ NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool L69 7BE, UK.
¹⁴ Faculty of Health Sciences, University of Buea, PO Box 63, Buea, Cameroon.
¹⁵ Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, P. O. Box LG 581, Legon, Ghana.
¹⁶ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut 06510, USA.
¹⁷ NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
¹⁸ Yale Institute for Global Health, Yale University, New Haven, Connecticut 06510, USA.

Abstract

G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, 5 years after the introduction of the Rotarix rotavirus vaccine. Here, we analysed representative twenty-seven whole genome sequences (G3P[4], n = 20; G3P[6], n = 1; and G3P[8], n = 6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each ribonucleic acid (RNA) segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1, and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease-burden settings to inform disease prevention and control.

Keywords: G3 strains; Malawi; Rotarix vaccine; genotype re-emergence; importation; phylodynamic; reassortment; rotavirus; sub-Saharan Africa; whole genome sequencing.