RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China

Zhu, Wentao; Yang, Jing; Lu, Shan; Jin, Dong; Pu, Ji; Wu, Shusheng; Luo, Xu; Liu, Liyun; Li, Zhenjun; Xu, Jianguo

doi:10.3389/fmicb.2022.780651

Cited by 10 publications

(9 citation statements)

References 59 publications

(74 reference statements)

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“…Both the RNA1 (RdRp) and RNA2 segments were identified, including two sequences with the complete RdRp. Nodavirus CP01/aus/1 and CP02/aus/1 were related to a nodavirus sampled from birds in China (Zhu et al, 2022) and most likely belong to the same viral species, although these fragments were only 476 and 232 amino acids, respectively. The nodavirus CP07/aus/1 RdRp segment was related to a nodavirus from arthropod hosts from China (Fig.…”

Section: Resultsmentioning

confidence: 99%

Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses

Brussel

Mahar

Ortiz-Báez

et al. 2022

Preprint

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Bats are important reservoirs for viruses of public health and veterinary concern. Virus studies in Australian bats usually target the families Paramyxoviridae, Coronaviridae and Rhabdoviridae, with little known about their overall virome composition. We used metatranscriptomic sequencing to characterise the faecal virome of grey-headed flying foxes from three colonies in urban/suburban locations from two Australian states. We identified viruses from three mammalian-infecting (Coronaviridae, Caliciviridae, Retroviridae) and one possible mammalian-infecting (Birnaviridae) family. Of particular interest were a novel bat betacoronavirus (subgenus Nobecovirus) and a novel bat sapovirus (Caliciviridae), the first identified in Australian bats, as well as a potentially exogenous retrovirus. The novel betacoronavirus was detected in two sampling locations 1,375 km apart and falls in a viral lineage likely with a long association with bats. This study highlights the utility of unbiased sequencing of faecal samples for identifying novel viruses and revealing broad-scale patterns of virus ecology and evolution.

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Section: Resultsmentioning

confidence: 99%

Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses

Brussel

Mahar

Ortiz-Báez

et al. 2022

Preprint

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“…BLAST searches also identified type 6 IRESs in several members of the Tombusviridae , including isolates s42-k141_944859 (Chen et al, 2022) (Figure 9E), 241-k141_1067879 (GenBank: MZ218436.1), 281-k141_21179 (MZ218468.1), 294-k141_79309 (MZ218531.1), 309R-k141_368388 (MZ218496.1), and the Solemoviridae sp. isolate YSN9007 (MW826524.1) [65]. They are ∼180 nt-long and are positioned to promote translation of the capsid protein.…”

Section: Resultsmentioning

confidence: 99%

Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites

Abaeva,

Pestova,

Hellen

2024

Preprint

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Viral internal ribosomal entry sites (IRESs) form several classes that use distinct mechanisms to mediate end-independent initiation of translation. The origin of viral IRESs is a longstanding question. The simplest IRESs comprise tandem pseudoknots and occur in the intergenic region (IGR) of vDicistroviridae genomes (order vPicornavirales). Larger IGR IRESs contain additional elements that determine specific properties such as binding to the head of the ribosomal 40S subunit. Metagenomic analyses reported here identified novel groups of structurally distinct IGR-like IRESs. The smallest of these (~120nt long) comprise three pseudoknots and bind directly to the ribosomal P site. Others are up to 260nt long: insertions occurred at specific loci, possibly reflecting non-templated nucleotide insertion during replication. Various groups can be arranged in order, differing by the cumulative addition of single structural elements, suggesting an accretion mechanism for the structural elaboration of IRESs. Identification of chimeric IRESs implicates recombinational exchange of domains as a second mechanism for the diversification of IRES structure. Recombination likely also accounts for the presence of IGR-like IRESs at the 5 prime-end of some dicistrovirus-like genomes (e.g. Hangzhou dicistrovirus 3) and in the RNA genomes of Tombusviridae (order Tolivirales), Marnaviridae (order Picornavirales), and the Ripiresk picorna-like clade (order Picornavirales).

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“…A previous study conducted metatranscriptomic sequencing of fecal samples from 56 bird species and 91 small mammals, including shrews, rats, hamsters, and pikas, to characterize the RNA virome. In this study, 12 vertebrate RNA viruses were identified, exhibiting less than 40% amino acid identity to known viruses [ 50 ]. Another study focused on the viromes of herbivorous animals, including camels, cattle, and donkeys, in the northwest plateau of China, revealing diversity differences among regions and species [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Luo,

Guan,

et al. 2024

Viruses

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Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai–Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

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RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China

Cited by 10 publications

References 59 publications

Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses

Faecal virome of the Australian grey-headed flying fox from urban/suburban environments contains novel coronaviruses, retroviruses and sapoviruses

Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

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