Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.
Colombo Municipal Council, Colombo, Sri Lanka.
J Virol Methods. 2022 Feb;300:114374. doi: 10.1016/j.jviromet.2021.114374. Epub 2021 Nov 22.
Although active surveillance SARS-CoV-2 variants of concern (VOCs) is required for proper outbreak control measures, many lower income countries find it challenging to detect VOCs by carrying genomic sequencing alone, due to limited resources.
VOCs can also be identified by the unique mutations in the spike protein by real-time PCR that detect these single nucleotide polymorphisms (SNPs). We used a multiplex, real-time PCR assay for detection of these SNPs for identification of the prevalence of different SARS-CoV-2 VOCs in 16/26 districts in Sri Lanka.
Of the 664/934 that were subjected to the multiplex qRT-PCR, 638 (96.1 %) detected L452R and K417 in the channels and were identified as the delta variant. 25 samples (3.9 %) detected N501Y, with K417 were considered as the alpha variant. Of 10/16 districts in Sri Lanka, the delta variant was the only VOC detected.
This multiplex real-time qRT-PCR which identifies certain SNPs specific to the VOCs appears to be a fast, cheaper and less technically demanding method to generate data regarding the spread of different SARS-CoV-2 variants, and is a suitable method for lower income countries, to supplement the data generated by genomic sequencing.
尽管需要对 SARS-CoV-2 关注变异株（VOC）进行主动监测，以采取适当的疫情控制措施，但由于资源有限，许多低收入国家仅通过基因组测序来发现 VOC 存在挑战。
通过实时 PCR 检测这些单核苷酸多态性（SNPs）也可以识别 Spike 蛋白中的独特突变来识别 VOC。我们使用多重实时 PCR 检测这些 SNP，以确定斯里兰卡 16/26 个地区不同 SARS-CoV-2 VOC 的流行情况。
在接受多重 qRT-PCR 检测的 664/934 例中，638 例（96.1%）在通道中检测到 L452R 和 K417，被鉴定为德尔塔变异株。25 例（3.9%）检测到 N501Y 和 K417，被认为是阿尔法变异株。在斯里兰卡的 10/16 个地区，仅检测到德尔塔变异株。
这种鉴定特定 VOC 的某些 SNP 的多重实时 qRT-PCR 似乎是一种快速、更便宜、技术要求更低的方法，可以生成有关不同 SARS-CoV-2 变体传播的数据，是一种适合低收入国家的方法，可以补充基因组测序生成的数据。
