Evaluation of SARS-CoV-2 Detection Efficiency by qRT-PCR Assays, Mainly on New Variants in East Java

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the novel coronavirus, SARS-CoV-2, which led to a global pandemic. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has undergone mutations, leading to the emergence of new variants worldwide, which may affect the accuracy of the diagnostic methods. This study aimed to identify the distribution of SARS-CoV-2 variants in East Java from 2021 to 2024 and analyze the mutation positions in the primer/probe targets of quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR). This study assessed the mismatches in WHO-recommended and other kits binding regions qRT-PCR assays against SARS-CoV-2 genome sequences from East Java through in-silico bioinformatics analysis. The results indicate that from 2021 to 2024, the distribution of SARS-CoV-2 variants in East Java has changed over time, including B.1.466.2, Alpha, Beta, Delta, and Omicron, along with various Omicron lineages. Primer and probe sequences from Sansure, Liferiver, US-CDC, EasyDiagnosis, and Pasteur displayed accurate matches (> 90%) with the SARS-CoV-2 sequences from East Java. On the other hand, many Omicron subvariants in East Java had high mismatches with the primer sequences from Charité-RdRp and CN-CDC-N. These findings highlight the importance of continuous surveillance of circulating variants and their mutations to ensure the effectiveness of diagnostics and response actions for emerging and re-emerging variants in the future.