Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus
Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of Severe Acute Respiratory Syndrome-Similar Coronavirus
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DOI：
10.1093/infdis/jiaa278
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发表时间：
2020-07-15
影响因子：
6.4
通讯作者：
Duan, Guangcai
中科院分区：
文献类型：
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作者：
Chen, Shuaiyin;Zheng, Xin;Duan, Guangcai
严重急性呼吸综合征冠状病毒（SARS - CoV）在2002 - 2003年的SARS疫情中被发现是一种新型病原体。这种病原体的出现和消失引发了有关其来源和进化的问题。在281株SARS - CoV、严重急性呼吸综合征冠状病毒2型（SARS - CoV - 2）以及SARS相关冠状病毒（SARSr - CoV）的基因组序列中，对一个约430bp且有规律变异的基因组区域（在AY390556.1中从27701bp到28131bp）进行了研究。这个约430bp的区域与ORF8基因重叠，容易发生缺失和核苷酸替换。其复杂性表明，需要一种针对与SARS类似冠状病毒（SARS - CoV、SARSr - CoV和SARS - CoV - 2）的新型基因分型方法。蝙蝠SARSr - CoV呈现3种基因型，其中0型仅在蝙蝠SARSr - CoV中出现，I型在SARS早期阶段存在，II型在所有SARS - CoV - 2中都能发现。这种基因分型在区分来自不同宿主和地理区域的SARS类似冠状病毒方面也显示出潜在用途。这个基因组区域对于预测疫情趋势和研究冠状病毒的进化具有重要意义。
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 similar to 430 bp genomic region (from 27 701 bp to 28 131 bp in AY390556.1) with regular variations was investigated. This similar to 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.