Phylogenetic analysis and evolution of feline bocavirus in Anhui Province, eastern China

Wang, Yong; Guo, Xingzhong; Li, Wei; Cui, Yongqiu; Zhang, Da; Xu, Fazhi; Jiang, Shudong; Zhou, Tianhong

doi:10.1016/j.cimid.2021.101676

Cited by 5 publications

(8 citation statements)

References 38 publications

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“…The represented major parent strain and the minor parent strain were strain PCLV-AH-25 (accession number: MZ773068/China) and strain 21 (accession number: JF713716.1/USA), respectively. Analysis of selection pressure showed that PCLV was subject to positive selection (Table 1), which may lead to the tendency of the virus to mutate and the continuous evolution of the virus, possibly prompting the emergence of new varieties [29,30]. In order to explore whether the selection would affect the immunogenicity of Rep, the B-cell epitopes were predicted (Table S4), and the results showed that two positive selection sites overlapped with immune epitopes in AH-23 (codons 142 and 211), six in AH-25 (codons 29, 142, 81, 211, 290 and 72) and two in AH-HB-2021(codons 47 and 211) (Figure 7).…”

Section: Recombination Selection Pressure and B-cell Antigenic Epitope Analysismentioning

confidence: 99%

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

Yang

Zhang

Liu

et al. 2021

Viruses

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Porcine circovirus-like virus (PCLV) is a type of circular Rep-encoding single-stranded DNA virus and may be associated with the development of diarrheal symptoms in pigs. In this study, we retrospectively analyzed three years of past cases in Anhui, China, and reported a case of hemorrhagic enteritis and death in a pregnant sow possibly caused by PCLV. In addition, we analyzed the evolutionary characteristics of PCLV and found that mutation, recombination and selective pressure all played an important role in the evolution of PCLV. We identified N15D and T17S as well as L56T, T58R, K59Q, M62R, L75I and R190K mutations in two different branches, and we noted recombination events in the Rep of a group of Chinese strains. Analysis of selection pressure revealed that PCLV gained more positive selection, indicating that the virus is in a continuous evolutionary state. The PR2 plot, ENC-plot and neutrality analysis showed a greater role of natural selection than that of mutational pressure in the formation of codon usage patterns. This study is the first to identify PCLV in sows with hemorrhagic dysentery and death, and it provides new epidemiological information on PCLV infection in pigs in China.

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Section: Recombination Selection Pressure and B-cell Antigenic Epitope Analysismentioning

confidence: 99%

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

Yang

Zhang

Liu

et al. 2021

Viruses

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“…Fifty‐seven and 24 HA gene sequences of H1N1 and H3N2 were downloaded from Genbank, respectively. Multiple sequence alignment was performed using MAFFT 15–17 . Maximum‐likelihood phylogenies were inferred using FastTree v2.1.11 18–20 .…”

Section: Methodsmentioning

confidence: 99%

“…Multiple sequence alignment was performed using MAFFT. [15][16][17] Maximum-likelihood phylogenies were inferred using FastTree v2.1.11. [18][19][20] Phylogenetic trees were visualized using iTOLv6.…”

Section: Bioinformatic Analysismentioning

confidence: 99%

Simultaneous identification of DNA and RNA pathogens using metagenomic sequencing in cases of severe acute respiratory infection

Xie,

Lin,

et al. 2024

Journal of Medical Virology

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Metagenomic next‐generation sequencing (mNGS) is a valuable technique for identifying pathogens. However, conventional mNGS requires the separate processing of DNA and RNA genomes, which can be resource‐ and time‐intensive. To mitigate these impediments, we propose a novel method called DNA/RNA cosequencing that aims to enhance the efficiency of pathogen detection. DNA/RNA cosequencing uses reverse transcription of total nucleic acids extracted from samples by using random primers, without removing DNA, and then employs mNGS. We applied this method to 85 cases of severe acute respiratory infections (SARI). Influenza virus was identified in 13 cases (H1N1: seven cases, H3N2: three cases, unclassified influenza type: three cases) and was not detected in the remaining 72 samples. Bacteria were present in all samples. Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii were detected in four influenza‐positive samples, suggesting coinfections. The sensitivity and specificity for detecting influenza A virus were 73.33% and 95.92%, respectively. A κ value of 0.726 indicated a high level of concordance between the results of DNA/RNA cosequencing and SARI influenza virus monitoring. DNA/RNA cosequencing enhanced the efficiency of pathogen detection, providing a novel capability to strengthen surveillance and thereby prevent and control infectious disease outbreaks.

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“…The CodonW (version 1.4.2) was used to calculate the Codon Adaptation Index (CAI) value, the effective number of codons (ENC), the percentage of nucleotide bases (A%, T%, C%, G%), and the third nucleotide of the basic synonymous codon (A3s%, T3s%, C3s%, G3s%) of the gene sequence (Wang et al, 2021a). Host codon usage was obtained from the codon usage database (http://www.kazusa.or.jp/codon/).…”

Section: Factors Affecting Codon Usagementioning

confidence: 99%

“…If the plots are located above or near the expected ENC curve, it indicates that codon usage preference is only affected by mutation pressure. If the genome is located far below the standard curve, it indicates that the codon usage preference is affected by other factors, such as natural selection (Wang et al, 2021a). Parity Rule 2 (PR2) plot was used to analyze the effects of mutation pressure and natural selection, with A3/A3 + T3 as the ordinate, G3/G3 + C3 is the abscissa.…”

Section: Factors Affecting Codon Usagementioning

confidence: 99%

Analyses of phylogeny and genetic evolution of Capripoxvirus in North and Northwest of China

Sun

et al. 2022

Preprint

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Capripoxviruses (CaPVs) mainly infect sheep, goats, and cattle, which cause rashes or knots, fever, and systemic papillae in flocks and herds. It is a highly infectious disease of major economic concern to the animal husbandry industry. This disease is widely spread all over the world, including China. In this study, we collected the tissue samples from goats, sheep, and cattle in the Northern and Northwestern of China, where the flocks and herds industries gather. Sequence alignment and phylogenetic tree analysis of GPCR, P32, and RPO30 showed that the two SPPV (Sheep poxvirus), two GTPV (Goat poxvirus), and one LSDV (Lumpy skin disease virus) strains were isolated in our works, respectively. Data of recombination analysis showed that SPPV strains usually has a recombination event in the GPCR gene. Except for GPCR genes, analysis of codon usage bias indicated that greater mutation pressure was found in GTPV and LSDV strains, and other genes were mainly affected by natural selection pressure in the evolutionary process. Selection pressure analysis also showed that SPPV, GTPV, and LSDV strains had a tendency to evolve toward adaptability. Taken together, this study shows how CaPVs have changed over time at the molecular and genetic levels in the North and Northwest of China. It also serves as a reference for future clinical and molecular research on CaPVs.

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Phylogenetic analysis and evolution of feline bocavirus in Anhui Province, eastern China

Cited by 5 publications

References 38 publications

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

Epidemiology and Evolution of Emerging Porcine Circovirus-like Viruses in Pigs with Hemorrhagic Dysentery and Diarrhea Symptoms in Central China from 2018 to 2021

Simultaneous identification of DNA and RNA pathogens using metagenomic sequencing in cases of severe acute respiratory infection

Analyses of phylogeny and genetic evolution of Capripoxvirus in North and Northwest of China

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