First identification and whole genome characterization of rotavirus C in pigs in Zambia

Hayato Harima; Yongjin Qiu; Michihito Sasaki; Joseph Ndebe; Kapila Penjaninge; Edgar Simulundu; Masahiro Kajihara; Aiko Ohnuma; Keita Matsuno; Naganori Nao; Yasuko Orba; Ayato Takada; Kanako Ishihara; William W Hall; Bernard M Hang'ombe; Hirofumi Sawa

doi:10.1016/j.virol.2024.110385

First identification and whole genome characterization of rotavirus C in pigs in Zambia

Virology. 2024 Dec 31:603:110385. doi: 10.1016/j.virol.2024.110385. Online ahead of print.

Authors

Hayato Harima¹, Yongjin Qiu², Michihito Sasaki³, Joseph Ndebe⁴, Kapila Penjaninge⁵, Edgar Simulundu⁶, Masahiro Kajihara⁷, Aiko Ohnuma⁸, Keita Matsuno⁹, Naganori Nao¹⁰, Yasuko Orba¹¹, Ayato Takada¹², Kanako Ishihara¹, William W Hall¹³, Bernard M Hang'ombe¹⁴, Hirofumi Sawa¹⁵

Affiliations

¹ Laboratory of Veterinary Public Health, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
² Laboratory of Parasitology, Department of Disease Control, Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, 060-0818, Japan.
³ Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan.
⁴ Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, 10101, Zambia.
⁵ Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, 10101, Zambia.
⁶ Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, 10101, Zambia; Macha Research Trust, Choma, 20100, Zambia.
⁷ Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.
⁸ Technical Office, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.
⁹ Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan; Division of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; One Health Research Center, Hokkaido University, Sapporo, 060-0818, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.
¹⁰ Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; One Health Research Center, Hokkaido University, Sapporo, 060-0818, Japan.
¹¹ Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan; One Health Research Center, Hokkaido University, Sapporo, 060-0818, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan.
¹² Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, 10101, Zambia; One Health Research Center, Hokkaido University, Sapporo, 060-0818, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, 10101, Zambia.
¹³ Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.
¹⁴ Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, 10101, Zambia; Department of Para-clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, 10101, Zambia.
¹⁵ Institute for Vaccine Research and Development, Hokkaido University, Sapporo, 001-0021, Japan; Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, 10101, Zambia; One Health Research Center, Hokkaido University, Sapporo, 060-0818, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan; Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, 10101, Zambia. Electronic address: [email protected].

PMID: 39756076
DOI: 10.1016/j.virol.2024.110385

Abstract

Rotavirus C (RVC) causes acute gastroenteritis in neonatal piglets. Despite the clinical importance of RVC infection, the distribution and prevalence in pig populations in most African countries remains unknown. In this study, we identified RVC in Zambian pigs by metagenomic analysis. The full genome sequence of the RVC revealed two different VP4 sequences, implying that two different RVC strains (ZP18-77-c1 and ZP18-77-c2) were present in the same sample. Genetic analyses demonstrated that all segments of ZP18-77-c1 and ZP18-77-c2 showed high nucleotide sequence identities (87.7-94.5%) to known porcine RVC strains, and ZP18-77-c1 and ZP18-77-c2 strains were assigned to genotype constellations, G1-P[4]/P[14]-I13-R5-C5-M1-A7-N9-T10-E5-H1. We further screened RVC genomes among pig feces collected in Zambia (n = 147) by RT-qPCR, and 78 samples (53.1%) were positive. This study demonstrated the first full genome sequence of African RVC strains with a relatively high prevalence of RVC infection in the pig populations in Zambia.

Keywords: Full genome sequence; Metagenomics; Phylogenetic analysis; Pig; Rotavirus C.