Abstract
The genome of the SARS-CoV-2 virus, the causal agent of the COVID-19 pandemic, has diverged due to multiple mutations since its emergence as a human pathogen in December 2019. Some mutations have defined several SARS-CoV-2 clades that seem to behave differently in terms of regional distribution and other biological features. Next-generation sequencing (NGS) approaches are used to classify the sequence variants in viruses from individual human patients. However, the cost and relative scarcity of NGS equipment and expertise in developing countries prevent studies aimed to associate specific clades and variants to clinical features and outcomes in such territories. As of March 2021, the GR clade and its derivatives, including the B.1.1.7 and B.1.1.28 variants, predominate worldwide. We implemented the post-PCR small-amplicon high-resolution melting analysis to genotype SARS-CoV-2 viruses isolated from the saliva of individual patients. This procedure was able to clearly distinguish two groups of samples of SARS-CoV-2-positive samples predicted, according to their melting profiles, to contain GR and non-GR viruses. This grouping of the samples was validated by means of amplification-refractory mutation system (ARMS) assay as well as Sanger sequencing.
Highlights
SARS-CoV-2 caused the ongoing pandemic severe respiratory coronavirus disease2019 (COVID-19), which was reported for the first time in China in December 2019 [1].During its replication, SARS-CoV-2 can undergo mutation, a change in the sequence of its genome
Due to the proofreading enzymatic activity encoded by the SARS-CoV-2 genome, single nucleotide substitutions occur at a slower rate in comparison to other RNA viruses [27]
It has been shown that recurrent deletions within the viral genomic segment encoding the Spike protein confer resistance to neutralizing antibodies [28], potentially diminishing the effectiveness of vaccines
Summary
SARS-CoV-2 caused the ongoing pandemic severe respiratory coronavirus disease2019 (COVID-19), which was reported for the first time in China in December 2019 [1].During its replication, SARS-CoV-2 can undergo mutation, a change in the sequence of its genome. SARS-CoV-2 caused the ongoing pandemic severe respiratory coronavirus disease. 2019 (COVID-19), which was reported for the first time in China in December 2019 [1]. SARS-CoV-2 can undergo mutation, a change in the sequence of its genome. Genomes that differ by one or more mutations are called variants. A dynamic lineage nomenclature has been adopted internationally in order to accommodate emerging variants and, at the same time, constrain the number and depth of hierarchical lineage labels [4]. Analysis of viral genomes—isolated from affected subjects from many countries—has allowed the identification of eight major clades: L (including the first Chinese cases reported), S, O, V, G and its derivatives GH, GV, GR and GRY [5,6,7]. The G clade is defined by the D614G mutation within the gene encoding the Spike (S) protein that binds its receptor in mammalian cells during infection
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