TY - JOUR

T1 - Substantial viral diversity in bats and rodents from East Africa

T2 - insights into evolution, recombination, and cocirculation

AU - Wang, Daxi

AU - Yang, Xinglou

AU - Ren, Zirui

AU - Hu, Ben

AU - Zhao, Hailong

AU - Yang, Kaixin

AU - Shi, Peibo

AU - Zhang, Zhipeng

AU - Feng, Qikai

AU - Nawenja, Carol Vannesa

AU - Obanda, Vincent

AU - Robert, Kityo

AU - Nalikka, Betty

AU - Waruhiu, Cecilia Njeri

AU - Ochola, Griphin Ochieng

AU - Onyuok, Samson Omondi

AU - Ochieng, Harold

AU - Li, Bei

AU - Zhu, Yan

AU - Si, Haorui

AU - Yin, Jiefang

AU - Kristiansen, Karsten

AU - Jin, Xin

AU - Xu, Xun

AU - Xiao, Minfeng

AU - Agwanda, Bernard

AU - Ommeh, Sheila

AU - Li, Junhua

AU - Shi, Zheng Li

N1 - Publisher Copyright: © The Author(s) 2024.

PY - 2024

Y1 - 2024

N2 - Background: Zoonotic viruses cause substantial public health and socioeconomic problems worldwide. Understanding how viruses evolve and spread within and among wildlife species is a critical step when aiming for proactive identification of viral threats to prevent future pandemics. Despite the many proposed factors influencing viral diversity, the genomic diversity and structure of viral communities in East Africa are largely unknown. Results: Using 38.3 Tb of metatranscriptomic data obtained via ultradeep sequencing, we screened vertebrate-associated viromes from 844 bats and 250 rodents from Kenya and Uganda collected from the wild. The 251 vertebrate-associated viral genomes of bats (212) and rodents (39) revealed the vast diversity, host-related variability, and high geographic specificity of viruses in East Africa. Among the surveyed viral families, Coronaviridae and Circoviridae showed low host specificity, high conservation of replication-associated proteins, high divergence among viral entry proteins, and frequent recombination. Despite major dispersal limitations, recurrent mutations, cocirculation, and occasional gene flow contribute to the high local diversity of viral genomes. Conclusions: The present study not only shows the landscape of bat and rodent viromes in this zoonotic hotspot but also reveals genomic signatures driven by the evolution and dispersal of the viral community, laying solid groundwork for future proactive surveillance of emerging zoonotic pathogens in wildlife. F1ZzYbc5Jf4XpNJGrZx-82 Video Abstract

AB - Background: Zoonotic viruses cause substantial public health and socioeconomic problems worldwide. Understanding how viruses evolve and spread within and among wildlife species is a critical step when aiming for proactive identification of viral threats to prevent future pandemics. Despite the many proposed factors influencing viral diversity, the genomic diversity and structure of viral communities in East Africa are largely unknown. Results: Using 38.3 Tb of metatranscriptomic data obtained via ultradeep sequencing, we screened vertebrate-associated viromes from 844 bats and 250 rodents from Kenya and Uganda collected from the wild. The 251 vertebrate-associated viral genomes of bats (212) and rodents (39) revealed the vast diversity, host-related variability, and high geographic specificity of viruses in East Africa. Among the surveyed viral families, Coronaviridae and Circoviridae showed low host specificity, high conservation of replication-associated proteins, high divergence among viral entry proteins, and frequent recombination. Despite major dispersal limitations, recurrent mutations, cocirculation, and occasional gene flow contribute to the high local diversity of viral genomes. Conclusions: The present study not only shows the landscape of bat and rodent viromes in this zoonotic hotspot but also reveals genomic signatures driven by the evolution and dispersal of the viral community, laying solid groundwork for future proactive surveillance of emerging zoonotic pathogens in wildlife. F1ZzYbc5Jf4XpNJGrZx-82 Video Abstract

KW - Evolution

KW - Metatranscriptome

KW - Viral surveillance

KW - Virome

U2 - 10.1186/s40168-024-01782-4

DO - 10.1186/s40168-024-01782-4

M3 - Journal article

C2 - 38600530

AN - SCOPUS:85189888408

VL - 12

JO - Microbiome

JF - Microbiome

SN - 2049-2618

IS - 1

M1 - 72

ER -