Dataset Information

Genomic Features and Evolution of the Parapoxvirus during the Past Two Decades.

ABSTRACT: Parapoxvirus (PPV) has been identified in some mammals and poses a great threat to both the livestock production and public health. However, the prevalence and evolution of this virus are still not fully understood. Here, we performed an in silico analysis to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between orf virus (ORFV) and other three species of PPVs, all PPVs showed almost identical nucleotide bias, that is GC richness. The structural analysis of PPV genomes showed the divergence of different PPV species, which may be due to the specific adaptation to their natural hosts. Additionally, we estimated the phylogenetic diversity of seven different genes of PPV. According to all available sequences, our results suggested that during 2010-2018, ORFV was the dominant virus species under the selective pressure of the optimal gene patterns. Furthermore, we found the substitution rates ranged from 3.56 × 10-5 to 4.21 × 10-4 in different PPV segments, and the PPV VIR gene evolved at the highest substitution rate. In these seven protein-coding regions, purifying selection was the major evolutionary pressure, while the GIF and VIR genes suffered the greatest positive selection pressure. These results may provide useful knowledge on the virus genetic evolution from a new perspective which could help to create prevention and control strategies.

SUBMITTER: Yao X

PROVIDER: S-EPMC7694016 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Genomic Features and Evolution of the Parapoxvirus during the Past Two Decades.

Yao Xiaoting X Pang Ming M Wang Tianxing T Chen Xi X Tang Xidian X Chang Jianjun J Chen Dekun D Ma Wentao W

Pathogens (Basel, Switzerland) 20201027 11

Parapoxvirus (PPV) has been identified in some mammals and poses a great threat to both the livestock production and public health. However, the prevalence and evolution of this virus are still not fully understood. Here, we performed an in silico analysis to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between orf virus (ORFV) and other three species of PPVs, all PPVs showed almost identical nucleotide bias, t ...[more]

PMID: 33120928

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Project description:BackgroundClinical practice is guided by guidelines in the era of evidence-based medicine to improve healthcare. The consistency between the strength of recommendations and the underlying quality of evidence in clinical guidelines and its evolution dynamically reflects the status of medical practice in important aspects. This study aimed to evaluate the levels of evidence (LOEs) supporting different classes of recommendations (CORs) in Chinese cardiovascular disease (CVD) guidelines between 2003 and 2021, and changes over time.MethodsClinical guideline documents on cardiovascular topics issued by leading professional organizations were retrieved in the Databases of SinoMed and Wanfang Med Online from inception to June 2021. All guidelines were screened through abstract and full-text reading, and included if satisfying the pre-specified criteria. 79 Chinese guideline documents on 12 sub-topics including a total of 5195 recommendations and the designated CORs/LOEs, were abstracted. The number of recommendations of Class Ⅰ, Class Ⅱ, Class Ⅲ, LOE A, LOE B, and LOE C were identified for each guideline document. The proportion of CORs, LOEs, and COR-LOE combinations in guidelines and the changes among those with ≥2 versions.FindingsA total of 79 guidelines were included in the analysis. When examining the status of current guidelines, among the 3325 recommendations derived from 59 documents during 2011-2021, 735 recommendations (22.1%) were classified as LOE A, 1280 (38.5%) as LOE B, and 1310 (39.4%) as LOE C. 596 recommendations (17.9%) were characterized as Class Ⅰ-LOE A, accounting for the majority of LOE A recommendations but only one-third of Class I recommendations. Evidence levels varied greatly across different sub-topics and individual guidelines. There are 9 guidelines on 5 sub-topics having ≥2 versions. When analyzing the changes over time, although an increase was observed in the total number of recommendations, the proportion of recommendations designated as Class Ⅰ-LOE A did not significantly improve (19.1% [current] vs 19.0% [prior], p = 0.97).InterpretationIn current Chinese CVD guidelines, the high level of evidence lacks, and its alignment with strong recommendations is deficient. Although it shows moderate improvements in certain major topics (e.g., coronary artery disease, interventional therapy, surgery) in the past two decades, the overall proportion of Class I-LOE A recommendations remains small, suggesting that conduction, and particularly translation, of high-quality studies like RCTs addressing CVDs-related questions are still essential and demanded, especially for areas with less attention.FundingThis study was supported by Beijing Nova Program from Beijing Municipal Science & Technology Commission (Z211100002121063, Z201100006820002); Fundamental Research Funds for the Central Universities (3332022023); National Key R&D Program of China (2020YFC2004705); CAMS Innovation Fund for Medical Sciences (2021-I2M-5-003); National Natural Science Foundation of China (81825003, 91957123, 82270376).

Dataset Information

Genomic Features and Evolution of the Parapoxvirus during the Past Two Decades.

Publications

Genomic Features and Evolution of the Parapoxvirus during the Past Two Decades.

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