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High prevalence of four novel astrovirus genotype species identified from rodents in China.

Abstract Astroviruses cause gastrointestinal and neurological infections in humans and animals. Since astrovirus is genetically diverse and different astrovirus genotypes can be found in the same animal species, astrovirus is a potential zoonotic threat to humans. In this study, we screened for astroviruses in rodents from Hong Kong, Hunan and Guangxi. Astrovirus was detected in 11.9 % (67/562) of rectal swab specimens. Phylogenetic analysis of the ORF1b region, which encodes the RdRp, showed that there were four distinct clusters (clusters A, B, C and D). Whole genome sequencing was performed for 11 representative strains from each of these four clusters. The mean amino acid genetic distances (p-dist) of full-length ORF2 were >0.634 between clusters A, B, C and other known astroviruses. The p-dist between clusters A and B, A and C, and B and C were 0.371-0.375, 0.517-0.549 and 0.524-0.555, respectively. Within cluster C, the p-dist between HN-014 and GX-006 was 0.372. Since strains with p-dist of ≥0.368 in ORF2 are now considered to be of separate genotypes species, cluster A, cluster B, cluster C-HN-014 and cluster C-GX-006 can be classified as novel genotype species. Cluster D was most closely related to the rodent astrovirus previously identified in Hong Kong. Since rodents live in close proximity to humans, interspecies jumping of these novel astroviruses may represent a threat to human health.
PMID
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Authors

Mayor MeshTerms

Genotype

Keywords
Journal Title the journal of general virology
Publication Year Start




PMID- 28537544
OWN - NLM
STAT- MEDLINE
DA  - 20170524
DCOM- 20170711
LR  - 20170713
IS  - 1465-2099 (Electronic)
IS  - 0022-1317 (Linking)
VI  - 98
IP  - 5
DP  - 2017 May
TI  - High prevalence of four novel astrovirus genotype species identified from rodents
      in China.
PG  - 1004-1015
LID - 10.1099/jgv.0.000766 [doi]
AB  - Astroviruses cause gastrointestinal and neurological infections in humans and
      animals. Since astrovirus is genetically diverse and different astrovirus
      genotypes can be found in the same animal species, astrovirus is a potential
      zoonotic threat to humans. In this study, we screened for astroviruses in rodents
      from Hong Kong, Hunan and Guangxi. Astrovirus was detected in 11.9 % (67/562) of 
      rectal swab specimens. Phylogenetic analysis of the ORF1b region, which encodes
      the RdRp, showed that there were four distinct clusters (clusters A, B, C and D).
      Whole genome sequencing was performed for 11 representative strains from each of 
      these four clusters. The mean amino acid genetic distances (p-dist) of
      full-length ORF2 were >0.634 between clusters A, B, C and other known
      astroviruses. The p-dist between clusters A and B, A and C, and B and C were
      0.371-0.375, 0.517-0.549 and 0.524-0.555, respectively. Within cluster C, the
      p-dist between HN-014 and GX-006 was 0.372. Since strains with p-dist of >/=0.368
      in ORF2 are now considered to be of separate genotypes species, cluster A,
      cluster B, cluster C-HN-014 and cluster C-GX-006 can be classified as novel
      genotype species. Cluster D was most closely related to the rodent astrovirus
      previously identified in Hong Kong. Since rodents live in close proximity to
      humans, interspecies jumping of these novel astroviruses may represent a threat
      to human health.
FAU - To, Kelvin K W
AU  - To KKW
AD  - 1Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of
      Hong Kong, Hong Kong SAR, PR China 2State Key Laboratory for Emerging Infectious 
      Diseases, The University of Hong Kong, Hong Kong SAR, PR China 4Research Centre
      of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
      3Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR
      China.
FAU - Chan, Wan-Mui
AU  - Chan WM
AD  - 1Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of
      Hong Kong, Hong Kong SAR, PR China.
FAU - Li, Kenneth S M
AU  - Li KSM
AD  - 1Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of
      Hong Kong, Hong Kong SAR, PR China.
FAU - Lam, Carol S F
AU  - Lam CSF
AD  - 1Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of
      Hong Kong, Hong Kong SAR, PR China.
FAU - Chen, Zhiwei
AU  - Chen Z
AD  - 2State Key Laboratory for Emerging Infectious Diseases, The University of Hong
      Kong, Hong Kong SAR, PR China 1Department of Microbiology, Li Ka Shing Faculty of
      Medicine, The University of Hong Kong, Hong Kong SAR, PR China 4Research Centre
      of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
      3Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR
      China.
FAU - Tse, Herman
AU  - Tse H
AD  - 3Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR
      China 2State Key Laboratory for Emerging Infectious Diseases, The University of
      Hong Kong, Hong Kong SAR, PR China 1Department of Microbiology, Li Ka Shing
      Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China
      4Research Centre of Infection and Immunology, The University of Hong Kong, Hong
      Kong SAR, PR China.
FAU - Lau, Susanna K P
AU  - Lau SKP
AD  - 3Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR
      China 2State Key Laboratory for Emerging Infectious Diseases, The University of
      Hong Kong, Hong Kong SAR, PR China 4Research Centre of Infection and Immunology, 
      The University of Hong Kong, Hong Kong SAR, PR China 1Department of Microbiology,
      Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR
      China.
FAU - Woo, Patrick C Y
AU  - Woo PCY
AD  - 1Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of
      Hong Kong, Hong Kong SAR, PR China 2State Key Laboratory for Emerging Infectious 
      Diseases, The University of Hong Kong, Hong Kong SAR, PR China 3Carol Yu Centre
      for Infection, The University of Hong Kong, Hong Kong SAR, PR China 4Research
      Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR,
      PR China.
FAU - Yuen, Kwok-Yung
AU  - Yuen KY
AD  - 1Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of
      Hong Kong, Hong Kong SAR, PR China 2State Key Laboratory for Emerging Infectious 
      Diseases, The University of Hong Kong, Hong Kong SAR, PR China 3Carol Yu Centre
      for Infection, The University of Hong Kong, Hong Kong SAR, PR China 4Research
      Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR,
      PR China.
LA  - eng
PT  - Journal Article
DEP - 20170525
PL  - England
TA  - J Gen Virol
JT  - The Journal of general virology
JID - 0077340
RN  - EC 2.7.7.48 (RNA Replicase)
SB  - IM
MH  - Animals
MH  - Astroviridae/*classification/genetics/*isolation & purification
MH  - Astroviridae Infections/epidemiology/*veterinary/virology
MH  - Cluster Analysis
MH  - Genome, Viral
MH  - *Genotype
MH  - Hong Kong/epidemiology
MH  - Phylogeny
MH  - Prevalence
MH  - RNA Replicase/genetics
MH  - Rectum/virology
MH  - Rodent Diseases/*epidemiology/*virology
MH  - Rodentia
MH  - Sequence Analysis, DNA
MH  - Sequence Homology
EDAT- 2017/05/26 06:00
MHDA- 2017/07/14 06:00
CRDT- 2017/05/25 06:00
AID - 10.1099/jgv.0.000766 [doi]
PST - ppublish
SO  - J Gen Virol. 2017 May;98(5):1004-1015. doi: 10.1099/jgv.0.000766. Epub 2017 May
      25.