In silico evaluation of the impact of Omicron variant of concern sublineage BA.4 and BA.5 on the sensitivity of RT‐qPCR assays for SARS‐CoV‐2 detection using whole genome sequencing
Authors: Sharma Divya , Notarte Kin Israel , Fernandez Rey Arturo , Lippi Giuseppe , Gromiha M. Michael , Henry Brandon M. 
Published: October 2022

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variant of concern (VoC) Omicron (B.1.1.529) has rapidly spread around the world, presenting a new threat to global public human health. Due to the large number of mutations accumulated by SARS‐CoV‐2 Omicron, concerns have emerged over potentially reduced diagnostic accuracy of reverse‐transcription polymerase chain reaction (RT‐qPCR), the gold standard diagnostic test for diagnosing coronavirus disease 2019 (COVID‐19). Thus, we aimed to assess the impact of the currently endemic Omicron sublineages BA.4 and BA.5 on the integrity and sensitivity of RT‐qPCR assays used for coronavirus disease 2019 (COVID‐19) diagnosis via in silico analysis. We employed whole genome sequencing data and evaluated the potential for false negatives or test failure due to mismatches between primers/probes and the Omicron VoC viral genome.MethodsIn silico sensitivity of 12 RT‐qPCR tests (containing 30 primers and probe sets) developed for detection of SARS‐CoV‐2 reported by the World Health Organization (WHO) or available in the literature, was assessed for specifically detecting SARS‐CoV‐2 Omicron BA.4 and BA.5 sublineages, obtained after removing redundancy from publicly available genomes from National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Avian Influenza Data (GISAID) databases. Mismatches between amplicon regions of SARS‐CoV‐2 Omicron VoC and primers and probe sets were evaluated, and clustering analysis of corresponding amplicon sequences was carried out.ResultsFrom the 1164 representative SARS‐CoV‐2 Omicron VoC BA.4 sublineage genomes analyzed, a substitution in the first five nucleotides (C to T) of the amplicon's 3′‐end was observed in all samples resulting in 0% sensitivity for assays HKUnivRdRp/Hel (mismatch in reverse primer) and CoremCharite N (mismatch in both forward and reverse primers). Due to a mismatch in the forward primer's 5′‐end (3‐nucleotide substitution, GGG to AAC), the sensitivity of the ChinaCDC N assay was at 0.69%. The 10 nucleotide mismatches in the reverse primer resulted in 0.09% sensitivity for Omicron sublineage BA.4 for Thai N assay. Of the 1926 BA.5 sublineage genomes, HKUnivRdRp/Hel assay also had 0% sensitivity. A sensitivity of 3.06% was observed for the ChinaCDC N assay because of a mismatch in the forward primer's 5′‐end (3‐nucleotide substitution, GGG to AAC). Similarly, due to the 10 nucleotide mismatches in the reverse primer, the Thai N assay's sensitivity was low at 0.21% for sublineage BA.5. Further, eight assays for BA.4 sublineage retained high sensitivity (more than 97%) and 9 assays for BA.5 sublineage retained more than 99% sensitivity.ConclusionWe observed four assays (HKUnivRdRp/Hel, ChinaCDC N, Thai N, CoremCharite N) that could potentially result in false negative results for SARS‐CoV‐2 Omicron VoCs BA.4 and BA.5 sublineages. Interestingly, CoremCharite N had 0% sensitivity for Omicron Voc BA.4 but 99.53% sensitivity for BA.5. In addition, 66.67% of the assays for BA.4 sublineage and 75% of the assays for BA.5 sublineage retained high sensitivity. Further, amplicon clustering and additional substitution analysis along with sensitivity analysis could be used for the modification and development of RT‐qPCR assays for detecting SARS‐CoV‐2 Omicron VoC sublineages.