Evaluation of SARS-CoV-2 detection efficiency by qRT-PCR assays, mainly on new variants in East Java

Loka, Ega Reviera Vida ORCID: https://orcid.org/0009-0003-5593-0109, Juniastuti, Juniastuti ORCID: https://orcid.org/0000-0002-1437-640X, Megasari, Ni Luh Ayu ORCID: https://orcid.org/0000-0002-4452-5250, Fitrianingsih, Avin Ainur ORCID: https://orcid.org/0000-0002-3571-114X and Lusida, Maria Inge ORCID: https://orcid.org/0000-0001-5039-0674 (2025) Evaluation of SARS-CoV-2 detection efficiency by qRT-PCR assays, mainly on new variants in East Java. Trends in Sciences, 22 (9). pp. 1-13. ISSN 2774-0226

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Abstract

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.

Item Type:	Journal Article
Keywords:	covid-19; in silico; molecular diagnostic; mutations; primer and probe mismatches; qrt-pcr; sars-cov-2; variants
Subjects:	11 MEDICAL AND HEALTH SCIENCES > 1108 Medical Microbiology > 110804 Medical Virology 11 MEDICAL AND HEALTH SCIENCES > 1108 Medical Microbiology > 110899 Medical Microbiology not elsewhere classified
Divisions:	Faculty of Medical and Health Sciences > Department of Medical Education
Depositing User:	Avin Ainur Fitrianingsih
Date Deposited:	10 Jul 2026 10:49

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