Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer

Liu, Qi; Wang, Hao; Ling, Yu; Yang, Shixing; Wang, Xiaochun; Zhou, Rui; Xiao, Yu; Chen, Xu; Yang, Jie; Fu, Weiguo; Zhang, Wen; Qi, Guilan

doi:10.1186/s12985-020-01332-y

Cited by 24 publications

(16 citation statements)

References 58 publications

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“…All sequences were aligned using CLUSTAL X (version 2.1) with the default settings. The aligned result was saved as a Nexus form file for constructing the phylogenetic tree using Bayes’ theorem in the Mrbayes 3.2.7 program ( Liu et al 2020 ). The Markov chain was run for a maximum of 1 million generations, in which every 50 generations were sampled, and the first 25% of Markov chain Monte Carlo (mcmc) samples were discarded as burnin.…”

Section: Methodsmentioning

confidence: 99%

Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui, China

Chen

et al. 2020

Polish Journal of Microbiology

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Porcine astroviruses (PAstVs) have wide distribution in swine herds worldwide. At present, five porcine astrovirus genotypes have been identified. In this study, using viral metagenomics, a novel PAstV strain (designated as Ahast) was identified in fecal samples from pigs in Anhui of China, and the complete genomic sequence of Ahast was obtained by assembling and PCR amplification. Genomic structural analysis indicated that Ahast had a typical ribosomal frameshifting signal, and some conserve amino acid motifs were also found in virally encoded proteins. Phylogenetic analysis and sequence comparison indicated that this virus belonged to porcine astrovirus genotype 4 (PAstV4), which formed a clade clustered with other PAstV4. Multiple recombinant events were confirmed by recombination analysis and indicated that Ahast was a potential recombinant. Epidemiological investigation indicated that PAstV4 has a 10.7% prevalence in this pig farm. The new recombinant identified in this study will be beneficial to comprehend the origin, genetic diversity, and evolution of porcine astroviruses in Anhui of China.

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Section: Methodsmentioning

confidence: 99%

Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui, China

Chen

et al. 2020

Polish Journal of Microbiology

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“…Genomic DNA was then extracted from approximately 200 mg of each semi-purified product using the commercial stool DNA Kit (TD601; Tianmo, Beijing, China). DNA samples were stored in 200 mL of the kit Solution Buffer at −20 C until ready for use (Liu et al, 2020).…”

Section: Dna Extractionmentioning

confidence: 99%

Investigation and molecular identification of Eimeria sp. sampled from captive forest musk deer

Ren

Zhao

et al. 2021

PeerJ

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Forest musk deer (Moschus berezovskii) is an endangered, protected species in China. Intestinal coccidiosis is a significant problem for captive forest musk deer. However, there are few reports on the prevalence and molecular characteristics of Eimeria sp. in forest musk deer. We sought to investigate the prevalence of Eimeria sp. in forest musk deer in the Sichuan and Shaanxi provinces in China. We also investigated the molecular characteristics of Eimeria sp. by analyzing the 18S rRNA gene. We collected a total of 328 fecal samples from forest musk deer on seven farms throughout the Sichuan and Shaanxi provinces. We extracted this parasite’s DNA and used this as a template for nested PCR amplification. The 18S rRNA gene fragment was associated with the plasmid vector, and these products were introduced into Escherichia coli (DH5α). The cultured bacterial solution was used as a PCR reaction template for identification purposes. We collected 328 fecal samples from forest musk deer in Lixian (n = 54), Maoxian (n = 52), Ma’erkang (n = 49), Dujiangyan (n = 55), Hanyuan (n = 41), Luding (n = 36) and Weinan (n = 41). One hundred ninety-eight (60.37%) fecal samples tested positive for Eimeria sp. . In our analysis of the 18S rRNA gene we found 34 types of Eimeria sp. with a similarity of 90.5–100%. We constructed a phylogenetic tree based on the parasite’s 18S rRNA gene sequence. Our findings indicated that the Eimeria sp. that parasitized the intestinal tract of forest musk deer was closely related to Eimeria alabamensis from Bos taurus and Eimeria ahsata from Ovis aries. To the best of our knowledge, ours was the first investigation and molecular identification of Eimeria sp. sampled from captive forest musk deer in China. Our results provide epidemiological data for the monitoring and prevention of Eimeria sp. in captive forest musk deer.

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“…ictvonline.org/ictv-reports/ictv_online_report/ssdna-viruses/w/circoviridae, accessed 10 July 2021]. Circoviruses and cycloviruses have been reported in various mammals, birds and arthropods [1][2][3][4][5][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23]. Circoviruses have also been detected in fish and reptiles [2,[23][24][25][26][27][28].…”

Section: Introductionmentioning

confidence: 99%

“…Based on genome-wide pairwise nt sequence identities and phylogenetic analysis, the International Committee on Taxonomy of Viruses (ICTV) has recognized at least 49 and 52 species within the genera Circovirus and Cyclovirus , respectively [ , accessed 10 July 2021]. Circoviruses and cycloviruses have been reported in various mammals, birds and arthropods [ 1 , 2 , 3 , 4 , 5 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 ]. Circoviruses have also been detected in fish and reptiles [ 2 , 23 , 24 , 25 , 26 , 27 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (Urva auropunctata): Identification of Novel Species

Gainor

Becker

Malik

et al. 2021

Viruses

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Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.

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Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer

Cited by 24 publications

References 58 publications

Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui, China

Identification and Characterization of a Novel Recombinant Porcine Astrovirus from Pigs in Anhui, China

Investigation and molecular identification of Eimeria sp. sampled from captive forest musk deer

Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (Urva auropunctata): Identification of Novel Species

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