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Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus.
J Infect Dis. 2020 06 29; 222(2):223-233.JI

Abstract

Severe acute respiratory syndrome coronavirus (SARS-CoV) was discovered as a novel pathogen in the 2002-2003 SARS epidemic. The emergence and disappearance of this pathogen have brought questions regarding its source and evolution. Within the genome sequences of 281 SARS-CoVs, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-related CoVs (SARSr-CoVs), a ~430 bp genomic region (from 27 701 bp to 28 131 bp in AY390556.1) with regular variations was investigated. This ~430 bp region overlaps with the ORF8 gene and is prone to deletions and nucleotide substitutions. Its complexity suggested the need for a new genotyping method for coronaviruses related to SARS-similar coronaviruses (SARS-CoV, SARSr-CoV, and SARS-CoV-2). Bat SARSr-CoV presented 3 genotypes, of which type 0 is only seen in bat SARSr-CoV, type I is present in SARS in the early phase, and type II is found in all SARS-CoV-2. This genotyping also shows potential usage in distinguishing the SARS-similar coronaviruses from different hosts and geographic areas. This genomic region has important implications for predicting the epidemic trend and studying the evolution of coronavirus.

Links

Authors+Show Affiliations

Zhengzhou University College of Public Health, Zhengzhou, China.

Taoharmony Biotech Ltd, Hangzhou, China.

Zhengzhou University College of Public Health, Zhengzhou, China.

Zhengzhou University College of Public Health, Zhengzhou, China.

Zhengzhou University College of Public Health, Zhengzhou, China.

Zhengzhou University College of Public Health, Zhengzhou, China. Duke University Medical Center, Duke University, Durham, North Carolina, USA.

Zhengzhou University College of Public Health, Zhengzhou, China.

First Affiliated Hospital, Zhengzhou University, Zhengzhou, China.

Beijing Ditan Hospital, Capital Medical University, Beijing, China.

Zhengzhou University College of Public Health, Zhengzhou, China.

MeSH

AnimalsBase SequenceBetacoronavirusChiropteraEutheriaEvolution, MolecularGenes, ViralGenetic VariationGenome, ViralHumansOpen Reading FramesPhylogenySevere acute respiratory syndrome-related coronavirusSARS-CoV-2Sequence AlignmentSequence DeletionSpike Glycoprotein, CoronavirusViral Matrix ProteinsViverridae

Pub Type(s)

Journal Article

Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32433742

Citation

Chen, Shuaiyin, et al. "Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus." The Journal of Infectious Diseases, vol. 222, no. 2, 2020, pp. 223-233.

Chen S, Zheng X, Zhu J, et al. Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus. J Infect Dis. 2020;222(2):223-233.

Chen, S., Zheng, X., Zhu, J., Ding, R., Jin, Y., Zhang, W., Yang, H., Zheng, Y., Li, X., & Duan, G. (2020). Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus. The Journal of Infectious Diseases, 222(2), 223-233. https://doi.org/10.1093/infdis/jiaa278

Chen S, et al. Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus. J Infect Dis. 2020 06 29;222(2):223-233. PubMed PMID: 32433742.

* Article titles in AMA citation format should be in sentence-case

TY - JOUR T1 - Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus. AU - Chen,Shuaiyin, AU - Zheng,Xin, AU - Zhu,Jingyuan, AU - Ding,Ronghua, AU - Jin,Yuefei, AU - Zhang,Weiguo, AU - Yang,HaiYan, AU - Zheng,Yingjuan, AU - Li,Xin, AU - Duan,Guangcai, PY - 2020/03/14/received PY - 2020/05/19/accepted PY - 2020/5/21/pubmed PY - 2020/7/8/medline PY - 2020/5/21/entrez KW - ORF8 gene KW - SARS-CoV KW - SARS-CoV-2 KW - genotyping method SP - 223 EP - 233 JF - The Journal of infectious diseases JO - J Infect Dis VL - 222 IS - 2 N2 - Severe acute respiratory syndrome coronavirus (SARS-CoV) was discovered as a novel pathogen in the 2002-2003 SARS epidemic. The emergence and disappearance of this pathogen have brought questions regarding its source and evolution. Within the genome sequences of 281 SARS-CoVs, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and SARS-related CoVs (SARSr-CoVs), a ~430 bp genomic region (from 27 701 bp to 28 131 bp in AY390556.1) with regular variations was investigated. This ~430 bp region overlaps with the ORF8 gene and is prone to deletions and nucleotide substitutions. Its complexity suggested the need for a new genotyping method for coronaviruses related to SARS-similar coronaviruses (SARS-CoV, SARSr-CoV, and SARS-CoV-2). Bat SARSr-CoV presented 3 genotypes, of which type 0 is only seen in bat SARSr-CoV, type I is present in SARS in the early phase, and type II is found in all SARS-CoV-2. This genotyping also shows potential usage in distinguishing the SARS-similar coronaviruses from different hosts and geographic areas. This genomic region has important implications for predicting the epidemic trend and studying the evolution of coronavirus. SN - 1537-6613 UR - https://www.unboundmedicine.com/medline/citation/32433742/Extended_ORF8_Gene_Region_Is_Valuable_in_the_Epidemiological_Investigation_of_Severe_Acute_Respiratory_Syndrome_Similar_Coronavirus_ DB - PRIME DP - Unbound Medicine ER -