The Rapid Screening of SARS-CoV-2 Variants can be an Alternative Solution for Low-Income Countries?

Zniber NM, Elbenaissi Y, Aadi Y, Elkochri S, Tagajdid MR, Agoudim S, Elannaz H, Laraqui A, Elmchichi B, Touil N, Ennibi K, Amine IL and Abi R
 

Department of Virology, Mohammed V Military Teaching Hospital, Mohammed V University, Morocco

^*Correspondance to: Zniber Mohamed Nabil 

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Abstract:

This research article assesses TIB MOLBIOL VirSNiP molecular screening tests for detecting SARSCoV- 2 variants. The analysis is then compared to high-throughput sequencing results obtained with the Ion Torrent platform. Swab samples from the nasopharynx and oropharynx of COVID- 19-positive patients were analyzed in the Virology Laboratory at the Military Teaching Hospital Mohamed V in Rabat. We used RT-PCR and Ion Torrent sequencing for variant detection. The VirSNiP assays detected spike mutations N460K, F486P, K444T, NSP12 Y273H, and NSP13 N268S. We assessed concordance between the two-method using Cohen’s kappa, sensitivity and specificity. The performance of the Spike N460K and K444T assays was excellent, with a sensitivity and specificity of 100%, thus achieving perfect concordance. Reliability in detecting variants was supported. Performance with the F486P assay was also satisfactory, recording a sensitivity of 89% and specificity of 100% (κ=0.92). However, the sensitivity of both NSP12 Y273H and NSP13 N268S mutation tests was lower at 11% and 30%, respectively, though they remained specific at 100%, with κ values in the moderate range (0.54 and 0.63, respectively). Finally, our results emphasizes that molecular screening is effective in the rapid and precise identification of COVID-19 variants, especially within resource limited institutions. Impact statement: This research article significantly contributes to the current understanding of molecular screening tests for detecting SARS-CoV-2 variants, especially in resource-limited settings. By comparing the performance of TIB MOLBIOL VirSNiP assays against high-throughput Ion Torrent sequencing, our study demonstrates that specific molecular assays, can achieve high sensitivity and specificity providing a reliable and rapid alternative to more expensive and timeconsuming methods. This work highlights the utility of molecular screening in offering timely and cost-effective genetic surveillance of SARS-CoV-2 variants, which is crucial for public health interventions and pandemic management. Our findings emphasize the importance of continuous validation and updating of molecular assays to adapt to the evolving genetic landscapes of SARSCoV- 2. The significance of this study lies in its potential to enhance diagnostic capabilities in lowresource settings, thereby supporting global efforts in tracking and controlling the spread of SARSCoV- 2 variants.

Keywords:

SARS-CoV-2; NGS sequencing; Variants; Molecular screening; Pandemic management; Real time RT-PCR

Cite the Article:

Zniber NM, Elbenaissi Y, Aadi Y, Elkochri S, Tagajdid MR, Agoudim S, et al. The Rapid Screening of SARSCoV- 2 Variants can be an Alternative Solution for Low-Income Countries?. Clin Case Rep Int. 2024; 8: 1697.