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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., 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

The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.

Clonorchiasis is a complex hepatobiliary disease caused by the foodborne parasite, Clonorchis sinensis (family Opisthorchiidae). This disease can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts, and has a major socioeconomic impact on ~ 35 million people predominantly in East Asia. Currently, no vaccine is available to prevent clonorchiasis, and repeated use of the only recommended drug, praziquantel (PZQ) increases the risk of developing drug resistance. Further understanding of the disease epidemiology relies on the knowledge of genetic variation of C. sinensis in endemic areas. Moreover, evidence of karyotypic variation within C. sinensis highlights the importance of comparing the genomes of geographically distinct isolates of this parasite. The two predominant research aims of this thesis were to decode the mitochondrial (mt) and nuclear genomes of a Korean isolate of C. sinensis and assess genetic variation, using high-throughput sequencing technologies and advanced bioinformatic workflows. The mt and nuclear genomes for a C. sinensis isolate from Korea (Cs-k2) were sequenced, assembled, characterised and compared with one or more isolates. In addition, a refined bioinformatic workflow was designed to infer high quality syntenic blocks between the nuclear genome and a previously published draft genome of another isolate from China. The results not only reveal a high level of nucleotide similarity within the syntenic regions, but also pinpoint variable genes that might be central to infection and/or adaptive process. The mt and nuclear genomes and the syntenic blocks now serve as a solid foundation for a future genetic analysis of C. sinensis. The mt genome, on one hand, confirmed the specific identity of the specimen, on the other hand, highlighted potential challenges with using mtDNA markers for genetic analyses. In contrast to the mt genome, the syntenic blocks of the nuclear genome exhibit major potential for future genetic studies due