Evidence map›Paper›PMID 31775738›Full record

ArticleBMC veterinary research2019

Bioinformatics analysis of capsid protein of different subtypes rabbit hemorrhagic disease virus.

Ruibin Qi, Jie Zhu, Qiuhong Miao, Aoxing Tang, Dandan Dong, Xiaoxue Wang, Guangqing Liu

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC veterinary research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 40% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 5 citations in OpenAlex.

  1. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 1 institution in 1 country.

Ruibin QiInnovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China.
Jie ZhuInnovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China.
Qiuhong MiaoInnovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China.
Aoxing TangInnovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China.
Dandan DongInnovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China.
Xiaoxue WangInnovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China.
Guangqing LiuInnovation Team of Small animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, People's Republic of China. liugq@shvri.ac.cn.ORCID http://orcid.org/0000-0002-7116-3689
Shanghai Veterinary Research Institute · CN

Funding

the Chinese Natural Sciences Foundation 31672572the Foundation of Shanghai Key Laboratory of Veterinary Biotechnology klab201712the Key Project of Agriculture Science and Technology of Shanghai 2016043the Key Research Project of National Science and Technology 2016YFD0500108
6 · The paper itself

Abstract

backgroundRabbit Hemorrhagic Disease Virus (RHDV) belongs to the Caliciviridae family, is a highly lethal pathogen to rabbits. Increasing numbers of studies have demonstrated the existence of antigenic variation in RHDV, leading to the emergence of a new RHDV isolate (RHDVb). However, the underlying factors determining the emergence of the new RHDV and its unpredictable epidemiology remain unclear. To investigate these issues, we selected more than 184 partial and/or complete genome sequences of RHDV from GenBank and analyzed their phylogenetic relationships, divergence, and predicted protein modification sites.

resultsPhylogenetic analysis showed that classic RHDV isolates, RHDVa, and RHDVb formed different clades. It's interesting to note that RHDVa being more closely related to classic RHDV than RHDVb, while RHDVb had a closer genetic relationship to Rabbit Calicivirus (RCV) than to classic RHDV isolates. Moreover, divergence analysis suggested that the accumulation of amino acid (aa) changes might be a consequence of adaptive diversification of capsid protein (VP60) during the division between classical RHDV, RHDVa, RHDVb, and RCV. Notably, the prediction of N-glycosylation sites suggested that RHDVb subtypes had two unique N-glycosylation sites (aa 301, 362) but lacked three other N-glycosylation sites (aa 45, 308, 474) displayed in classic RHDV and RHDVa VP60 implying this divergence of N-glycosylation sites in RHDV might affect viral virulence. Analysis of phosphorylation sites also indicated that some phosphorylation sites in RHDVa and RHDVb differed from those in classic RHDV, potentially related to antigenic variation in RHDV.

conclusionThe genetic relationship between RHDVb and RCV was closer than classic RHDV isolates. Moreover, compared to RHDV and RHDVa, RHDVb had two unique N-glycosylation sites but lacked three sites, which might affect the virulence of RHDV. These results may provide new clues for further investigations of the origin of new types of RHDV and the mechanisms of genetic variation in RHDV.

Indexed as

Genome, ViralCapsid ProteinsComputational BiologyGenetic VariationGlycosylationHemorrhagic Disease Virus, RabbitPhylogenySequence Analysis, ProteinCapsid ProteinsBioinformatics analysisRHDVRHDVaRHDVb

Identifiers

PMID31775738
PMCPMC6882040
OpenAlexW2989997103

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.