SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods

Abstract

Since the beginning of COVID-19 pandemic the Real Time sharing of genome sequences of circulating virus supported the diagnostics and surveillance of SARS-CoV-2 and its transmission dynamics. SARS-CoV-2 straightaway showed its tendency to mutate and adapt to the host, culminating in the emergence of variants; so it immediately became of crucial importance to be able to detect them quickly but also to be able to monitor in depth the changes on the whole genome to early identify the new possibly emerging variants. In this scenario, this manuscript aims to provide an overview of the existing methods for the identification of SARS-CoV-2 variants (from rapid method based on identification of one or more specific mutations to Whole Genome sequencing approach-WGS), taking into account limitations, advantages and applications of them in the field of diagnosis and surveillance of SARS-CoV-2.

Immunological Studies to Understand Hybrid/Recombinant Variants of SARS-CoV-2

“…This includes methods such as the SARS-CoV-2 variant assay involving RT-PCR and sequencing, the multitarget designed assay comprising of RT-PCR and analysis of the melting curve, and the multivariant deletion assay involving RT-PCR and qPCR, etc. [ 30 ].…”

“…With a large dataset of sequences of SARS-CoV-2 variants available to analyze the sequence of SARS-CoV-2, this technique is efficient in identifying the mutations and locus of recombination concerning the parent variant. The technique can be used for designing diagnostic approaches, as it is efficient in identifying the conserved domains and performing phylogenetic analysis [ 30 ].…”

“…Numerous commercial rapid assays have been designed for identifying the variants, such as the SARS-CoV-2 variant direct assay, that detects the mutations in the spike protein at the N501Y, E484K, E484Q, and L452R sites. In this method, the samples from the nasopharyngeal and nasal swabs can be used directly, without the requirement for the extraction of RNA [ 30 ].…”

Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance

“…Thus, determining the infecting variant may also be used for clinical decision-making for an individual patient. While next-generation sequencing (NGS) has arisen as the gold standard technology for genomic surveillance and variant discovery [ 4 ], the technology remains cost prohibitive for decentralized sequencing, particularly in small independent and resource-limited laboratories [ 5 ]. Illumina COVIDSeq™ is one of the most adopted methods for COVID-19 surveillance.…”

Optimization of the Illumina COVIDSeq™protocol for decentralized, cost-effective genomic surveillance

“…Keeping SARS-CoV-2 in the foreground, new lineages will likely emerge, and monitoring evolving variants is epidemiologically critical (Aleem et al, 2022; Anderson et al, 2021). While next-generation sequencing (NGS) has emerged as the gold standard technology for genomic surveillance and variant discovery (Berno et al, 2022), the technology remains cost prohibitive for de-centralized sequencing, particularly in small independent and resource-limited laboratories (Umunnakwe et al, 2022). Illumina COVIDSeq™ is one of the most utilized methods for COVID surveillance, but the application has been limited mainly to centralized surveillance programs.…”