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.

Keywords: COVID-19; SARS-CoV-2; SARS-CoV-2 pandemic; rapid methods; sequencing; surveillance; variants characterization.

Figure 1

Non-synonymous mutations of SARS-CoV-2 variants. Mutation frequencies and nucleotide positions are reported together with corresponding gene locations. Graphic representation of Spike gene principal domains is also represented.

Figure 2

Pipeline of sample analysis in epidemiological surveillance. The sample of different individuals are analysed with RT-PCR or Rapid Test. Only the sample positive to RT- PCR with adequate viral load (Ct < 33) are further analysed with Sanger, NGS or Real Time RT-PCR. The variant identified results are then send to the surveillance authority.