Article, 2024
Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation
Microbiome,
ISSN
2049-2618,
Volume 12,
1,
Page 72,
10.1186/s40168-024-01782-4
Contributors
Wang, Daxi
[1]
Yang, Xinglou
0000-0002-5317-8983
[2]
[3]
[4]
Ren, Zirui
[1]
Hu, Ben
[3]
[4]
Zhao, Hailong
[1]
Yang, Kaixin
[1]
[5]
Shi, Peibo
[1]
[5]
Zhang, Zhipeng
[1]
Feng, Qikai
[1]
[5]
Nawenja, Carol Vannesa
[3]
[5]
Obanda, Vincent O
[6]
Robert, Kityo
[7]
Nalikka, Betty
[7]
Waruhiu, Cecilia Njeri
[3]
Ochola, Griphin Ochieng
[3]
[8]
Onyuok, Samson Omondi
[3]
[8]
Ochieng, Harold
[3]
[8]
Li, Bei
0000-0003-0596-2957
[3]
Zhu, Yan
0000-0001-7342-3782
[3]
Si, Hao-Rui
[3]
Yin, Jiefang
[1]
Kristiansen, Karsten
[9]
Jin, Xin
[1]
Xu, Xun
[1]
Xiao, Minfeng
0000-0002-0507-7352
(Corresponding author)
[1]
Agwanda, Bernard Risky
0000-0003-4135-4537
(Corresponding author)
[8]
Ommeh, Sheila Cecily
0000-0002-0780-0399
(Corresponding author)
[10]
Li, Junhua
(Corresponding author)
[1]
Shi, Zhengli-Li
0000-0001-8089-163X
(Corresponding author)
[3]
[4]
Affiliations
- [1]
BGI Group (China)
[NORA names:
China; Asia, East];
- [2]
Hubei Jiangxia Lab, 430071, Wuhan, China
[NORA names:
China; Asia, East];
- [3]
Wuhan Institute of Virology
[NORA names:
China; Asia, East];
- [4]
Chinese Academy of Sciences
[NORA names:
China; Asia, East];
- [5]
University of Chinese Academy of Sciences
[NORA names:
China; Asia, East];
(... more)
- [6]
Kenya Wildlife Service
[NORA names:
Kenya; Africa];
- [7]
Makerere University
[NORA names:
Uganda; Africa];
- [8]
National Museums of Kenya
[NORA names:
Kenya; Africa];
- [9]
University of Copenhagen
[NORA names:
KU University of Copenhagen;
University; Denmark; Europe, EU; Nordic; OECD];
- [10]
University of Queensland
[NORA names:
Australia; Oceania; OECD]
(less)
Abstract
BackgroundZoonotic 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.ResultsUsing 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.ConclusionsThe 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-82Video Abstract
Keywords
Africa,
Circoviridae,
ConclusionsThe,
ConclusionsThe present study,
Coronaviridae,
East,
East Africa,
Kenya,
Uganda,
bats,
cocirculation,
community,
conservation,
data,
dispersal limitation,
dispersion,
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entry proteins,
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flow,
frequent recombination,
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host-related variables,
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limitations,
low host specificity,
metatranscriptomic data,
mutations,
pandemic,
pathogens,
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prevent future pandemics,
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protein,
public health,
recombination,
recurrent mutations,
replication-associated protein,
rodents,
sequence,
signature,
socioeconomic problems,
solid groundwork,
species,
specificity,
specificity of viruses,
structure,
structure of viral communities,
study,
surveillance,
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ultradeep,
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viral diversity,
viral entry proteins,
viral families,
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virome,
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wild,
wildlife,
wildlife species,
zoonotic pathogens
Funders
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