Dataset Information

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation.

ABSTRACT:

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. Video Abstract.

SUBMITTER: Wang D

PROVIDER: S-EPMC11005217 | biostudies-literature | 2024 Apr

REPOSITORIES: biostudies-literature

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Publications

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation.

Wang Daxi D Yang Xinglou X Ren Zirui Z Hu Ben B Zhao Hailong H Yang Kaixin K Shi Peibo P Zhang Zhipeng Z Feng Qikai Q Nawenja Carol Vannesa CV Obanda Vincent V Robert Kityo K Nalikka Betty B Waruhiu Cecilia Njeri CN Ochola Griphin Ochieng GO Onyuok Samson Omondi SO Ochieng Harold H Li Bei B Zhu Yan Y Si Haorui H Yin Jiefang J Kristiansen Karsten K Jin Xin X Xu Xun X Xiao Minfeng M Agwanda Bernard B Ommeh Sheila S Li Junhua J Shi Zheng-Li ZL

Microbiome 20240410 1

<h4>Background</h4>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.<h4>Results</h4>Using 38.3 Tb of metatranscriptomic dat ...[more]

PMID: 38600530

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Project description:One of the main goals of community ecology is to measure the relative importance of environmental filters to understand patterns of species distribution at different temporal and spatial scales. Likewise, the identification of factors that shape symbiont metacommunity structures is important in disease ecology because resulting structures drive disease transmission. We tested the hypothesis that distributions of virus species and viral families from rodents and bats are defined by shared responses to host phylogeny and host functional characteristics, shaping the viral metacommunity structures at four spatial scales (Continental, Biogeographical, Zoogeographical, and Regional). The contribution of host phylogeny and host traits to the metacommunity of viruses at each spatial scale was calculated using a redundant analysis of canonical ordering (RDA). For rodents, at American Continental scale the coherence of viral species metacommunity increased while the spatial scale decreased and Quasi-Clementsian structures were observed. This pattern suggests a restricted distribution of viruses through their hosts, while in the Big Mass (Europe, Africa, and Asia), the coherence decreased as spatial scale decreased. Viral species metacommunities associated with bats was dominated by random structures along all spatial scales. We suggest that this random pattern is a result of the presence of viruses with high occupancy range such as rabies (73%) and coronavirus (27%), that disrupt such structures. At viral family scale, viral metacommunities associated with bats showed coherent structures, with the emergence of Quasi- Clementsian and Checkerboard structures. RDA analysis indicates that the assemblage of viral diversity associated with rodents and bats responds to phylogenetic and functional characteristics, which alternate between spatial scales. Several of these variations could be subject to the spatial scale, in spite of this, we could identify patterns at macro ecological scale. The application of metacommunity theory at symbiont scales is particularly useful for large-scale ecological analysis. Understanding the rules of host-virus association can be useful to take better decisions in epidemiological surveillance, control and even predictions of viral distribution and dissemination.Electronic supplementary materialSupplementary material is available for this article at 10.1556/168.2018.19.2.9 and is accessible for authorized users.

Dataset Information

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation.

Background

Results

Conclusions

Publications

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation.

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