Evidence map›Paper›PMID 31026605›Full record

ArticleInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2019

Detection and spike gene characterization in porcine deltacoronavirus in China during 2016-2018.

Yu Zhang, Yao Cheng, Gang Xing, Jing Yu, Ao Liao, Liuyang Du, Jing Lei, Xue Lian, Jiyong Zhou, Jinyan Gu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.

0numbers the graph read from it
0cells of the map it votes in
22citing papers in PubMed
–field-weighted citation impact
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

22 citing papers in PubMed.

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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

10 authors.

Yu ZhangMOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
Yao ChengMOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
Gang XingMOA key laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
Jing YuMOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
Ao LiaoMa'anshan Shiji Animal Health Management Co. Ltd, Anhui, China.
Liuyang DuMOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
Jing LeiMOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
Xue LianJiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
Jiyong ZhouMOA key laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
Jinyan GuMOE Joint International Research Laboratory of Animal Health and Food Safety, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; MOA key laboratory of Animal Virology, Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: gjy@njau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Porcine deltacoronavirus (PDCoV) has been emerging in several swine-producing countries for years. In our study, 719 porcine diarrhoea samples from 18 provinces in China were collected for PDCoV and porcine epidemic diarrhoea virus (PEDV) detection. The epidemiological survey revealed that the positive rates of PDCoV, PEDV and coinfection were 13.07%, 36.72% and 4.73%, respectively. The entire spike (S) genes of eleven detected PDCoV strains were sequenced. Phylogenetic analysis showed that the majority of PDCoVs could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage. The China and the Viet Nam/Laos/Thailand lineages showed much greater genetic divergences than the USA/Japan/South Korea lineage. The present study detected one new monophyletic branch that contained three PDCoVs from China, and this branch was separated from the China lineage but closely related to the Viet Nam/Laos/Thailand lineage. The strain CH-HA2-2017, which belongs to this new branch, had a possible recombination event between positions 27 and 1234. Significant amino acid substitutions of PDCoV S proteins were analysed and displayed with a three-dimensional cartoon diagram. The visual spatial location of these substitutions gave a conformational-based reference for further studies on the significance of critical sites on the PDCoV S protein.

Indexed as

AnimalsChinaCoronavirusGene Expression Regulation, ViralGenome, ViralPharmacogenomic VariantsPhylogenyPolymerase Chain ReactionSpike Glycoprotein, CoronavirusSwineSwine DiseasesSpike Glycoprotein, CoronavirusAmino acid substitutionsPhylogenetic analysisPorcine deltacoronavirusSpike gene

Identifiers

PMID31026605
PMCPMC7106087

What OpenQuestion holds

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Registered trials

None linked

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.