Molecular Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 Isolates From Central Inner Sardinia

Abstract

BackgroundThe SARS-CoV-2 pandemic stimulated an outstanding global sequencing effort, which allowed to monitor viral circulation and evolution. Nuoro province (Sardinia, Italy), characterized by a relatively isolated geographical location and a low population density, was severely hit and displayed a high incidence of infection.MethodsAmplicon approach Next Generation Sequencing and subsequent variant calling in 92 respiratory samples from SARS-CoV-2 infected patients involved in infection clusters from March 2020 to May 2021.ResultsPhylogenetic analysis displayed a coherent distribution of sequences in terms of lineage and temporal evolution of pandemic. Circulating lineage/clade characterization highlighted a growing diversity over time, with an increasingly growing number of mutations and variability of spike and nucleocapsid proteins, while viral RdRp appeared to be more conserved. A total of 384 different mutations were detected, of which 196 were missense and 147 synonymous ones. Mapping mutations along the viral genome showed an irregular distribution in key genes. S gene was the most mutated gene with missense and synonymous variants frequencies of 58.8 and 23.5%, respectively. Mutation rates were similar for the S and N genes with one mutation every ∼788 nucleotides and every ∼712 nucleotides, respectively. Nsp12 gene appeared to be more conserved, with one mutation every ∼1,270 nucleotides. The frequency of variant Y144F in the spike protein deviated from global values with higher prevalence of this mutation in the island.ConclusionThe analysis of the 92 viral genome highlighted evolution over time and identified which mutations are more widespread than others. The high number of sequences also permits the identification of subclusters that are characterized by subtle differences, not only in terms of lineage, which may be used to reconstruct transmission clusters. The disclosure of viral genetic diversity and timely identification of new variants is a useful tool to guide public health intervention measures.

Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern

“…Deletions, insertions, frameshift variants, and up/downstream variants were much rarer. This observation is also in line with the finding of Malune et al, whose study reported less than 10% of these mutations [70].…”

Recapping the Features of SARS-CoV-2 and Its Main Variants: Status and Future Paths

“…A possible reason is the dissociation of polymerase complex, now that these viruses present a high rate of RNA recombination during replication [ 19 , 22 ]. Nevertheless, some next-generation sequencing (NGS) approaches have analyzed the evolution of lineages in this short period of time, identifying an increasing number of mutations and variability in S and N proteins, but more conserved sequences in RdRp [ 23 ]. Importantly, these mutations can lead to an enhanced replication and transmissibility of the virus, and in turn this can favor further mutations, thus explaining the success and rapid evolution of SARS-CoV-2 [ 24 ].…”

“…The rapid evolution has shown that many ramifications can arise from the same lineage; for example, the Delta variant has produced approximately 200 subvariants, and Omicron has 4 prominent subvariants with great spreading ability. As previously mentioned, most common mutations that can be found are within S and N proteins [ 23 ].…”

Origin, Genetic Variation and Molecular Epidemiology of SARS-CoV-2 Strains Circulating in Sardinia (Italy) during the First and Second COVID-19 Epidemic Waves

“…It is, therefore, not surprising that Sardinia was one of the last Italian regions infected during the first wave (March–May 2020), with one of the lowest COVID-19 cases incidences reported at that time (79.9 cases/100,000 inhabitants). Furthermore, its socio-geographic features—insularity, large rural areas, limited connectivity between major cities and low population density—have created a peculiar epidemiological scenario [ 13 , 17 , 19 , 20 ]. Tourism flow to the island during the summer season (June–September 2020) was restored after the lockdown measures, causing a sharp increase in the number of infections, and during the second wave Sardinia became the first Italian region categorized as high risk by the European Centre for Disease Prevention and Control (ECDC) [ 21 ].…”