Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
Substantial viral diversity in bats and rodents from East Africa : insights into evolution, recombination, and cocirculation. / Wang, Daxi; Yang, Xinglou; Ren, Zirui; Hu, Ben; Zhao, Hailong; Yang, Kaixin; Shi, Peibo; Zhang, Zhipeng; Feng, Qikai; Nawenja, Carol Vannesa; Obanda, Vincent; Robert, Kityo; Nalikka, Betty; Waruhiu, Cecilia Njeri; Ochola, Griphin Ochieng; Onyuok, Samson Omondi; Ochieng, Harold; Li, Bei; Zhu, Yan; Si, Haorui; Yin, Jiefang; Kristiansen, Karsten; Jin, Xin; Xu, Xun; Xiao, Minfeng; Agwanda, Bernard; Ommeh, Sheila; Li, Junhua; Shi, Zheng Li.
In: Microbiome, Vol. 12, No. 1, 72, 2024.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
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 -
ID: 388830036