Trends of Mismatches in Real-Time RT-PCR Assays Developed by the National Institute of Infectious Diseases, Japan for Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2.

IF 1.3 4区 医学 Q4 INFECTIOUS DISEASES
Kazuya Shirato, Makoto Ujike, Miyuki Kawase
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Abstract

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2021 and gradually overtook the Delta variant, which was the predominant variant at that time. The Omicron variant has been consecutively replaced by related sublineages. The real-time RT-PCR assays developed by the National Institute of Infectious Diseases (NIID), Japan (i.e., the NIID-N2 and NIID-S2 assays) are the reference assays that have been used in Japan since the outbreak of SARS-CoV-2. To evaluate the applicability of the NIID assays for the Omicron variants, trends in the prevalence of nucleotide mismatches in the primer/probe sequences were traced using sequences registered in the Global Initiative on Sharing Avian Influenza Data database. Approximately 99% of the deposited Omicron variant sequences did not have any mismatches in the NIID assay primer/probes from January to August 2022. This indicates that the NIID assays have been able to detect the changing SARS-CoV-2 Omicron variants.

日本国立传染病研究所开发的严重急性呼吸综合征冠状病毒组粒变异实时RT-PCR检测方法的错配趋势
严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)的Omicron变体于2021年底出现,并逐渐取代当时占主导地位的Delta变体。基因组变体已连续被相关的亚谱系所取代。日本国立传染病研究所(NIID)开发的实时RT-PCR检测方法(即NIID- n2和NIID- s2检测方法)是自SARS-CoV-2爆发以来日本使用的参考检测方法。为了评估NIID检测对Omicron变异的适用性,利用全球共享禽流感数据倡议数据库中注册的序列,追踪了引物/探针序列中核苷酸错配的流行趋势。在2022年1月至8月期间,大约99%的沉淀的Omicron变异序列在NIID检测引物/探针中没有任何错配。这表明NIID检测已经能够检测到不断变化的SARS-CoV-2基因组变体。
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来源期刊
CiteScore
4.50
自引率
4.50%
发文量
172
审稿时长
2 months
期刊介绍: Japanese Journal of Infectious Diseases (JJID), an official bimonthly publication of National Institute of Infectious Diseases, Japan, publishes papers dealing with basic research on infectious diseases relevant to humans in the fields of bacteriology, virology, mycology, parasitology, medical entomology, vaccinology, and toxinology. Pathology, immunology, biochemistry, and blood safety related to microbial pathogens are among the fields covered. Sections include: original papers, short communications, epidemiological reports, methods, laboratory and epidemiology communications, letters to the editor, and reviews.
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