The Spread of SARS-CoV-2 Omicron Variant in CALABRIA: A Spatio-Temporal Report of Viral Genome Evolution

Abstract

We investigated the evolution of SARS-CoV-2 spread in Calabria, Southern Italy, in 2022. A total of 272 RNA isolates from nasopharyngeal swabs of individuals infected with SARS-CoV-2 were sequenced by whole genome sequencing (N = 172) and/or Sanger sequencing (N = 100). Analysis of diffusion of Omicron variants in Calabria revealed the prevalence of 10 different sub-lineages (recombinant BA.1/BA.2, BA.1, BA.1.1, BA.2, BA.2.9, BA.2.10, BA.2.12.1, BA.4, BA.5, BE.1). We observed that Omicron spread in Calabria presented a similar trend as in Italy, with some notable exceptions: BA.1 disappeared in April in Calabria but not in the rest of Italy; recombinant BA.1/BA.2 showed higher frequency in Calabria (13%) than in the rest of Italy (0.02%); BA.2.9, BA.4 and BA.5 emerged in Calabria later than in other Italian regions. In addition, Calabria Omicron presented 16 non-canonical mutations in the S protein and 151 non-canonical mutations in non-structural proteins. Most non-canonical mutations in the S protein occurred mainly in BA.5 whereas non-canonical mutations in non-structural or accessory proteins (ORF1ab, ORF3a, ORF8 and N) were identified in BA.2 and BA.5 sub-lineages. In conclusion, the data reported here underscore the importance of monitoring the entire SARS-CoV-2 genome.

The spike-specific TCRβ repertoire shows distinct features in unvaccinated or vaccinated patients with SARS-CoV-2 infection

“…We enrolled 14 consecutive patients tested positive for SARS-CoV-2 with mild to severe COVID-19 [ 23 ] from January 24th to July 7th, 2022. At that time the Omicron variants were predominant in our setting in Calabria region, Southern Italy [ 24 ]. Patients with mild COVID-19 symptoms for a maximum of 7 days who did not require oxygen support presented to the center dedicated to early therapies for COVID-19 [ 25 ] to receive neutralizing monoclonal antibodies (moAbs) or antivirals (i.e., remdesivir, nirmatrelvir/ritonavir or molnupiravir).…”

Evolution of in-hospital patient characteristics and predictors of death in the COVID-19 pandemic across four waves: are they moving targets with implications for patient care?

“…Multicentric studies are needed to understand if our results are confirmed in different settings across Italy. Second, despite the fact that there was a lack of data about SARS-CoV-2 variants of concern (VoCs) and subvariants in individual patients, the general picture and evolution are well known in our region since an epidemiological survey coordinated by our center demonstrated that in August 2021, Delta was the only circulating variant, while as of January 2022, Omicron subvariants emerged and took over Delta ( 45 , 46 ). Therefore, SARS-CoV-2 variants and subvariants do not appear to be a reasonable explanation for the increase of the inpatients mortality during the fourth wave, because Omicron variants/subvariants prevailed in this period, being already associated with reduced virulence, particularly in patients who received full vaccination course ( 47 ).…”

Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy

“…Thus, the L5F is disadvantageous for the SARS-CoV-2 virus because the mutated epitope could enhance CD8 T cell recognition and killing through this improved interaction [63]. Additionally, it was the only unusual substitution to appear in BA.2 and BA.5 sub-lineages among 272 positive samples isolated in Southern Italy [64]. The L18F substitution is of significance because it has been found to compromise binding of neutralizing antibodies, allowing a much faster propagation in the presence of plasma antibodies collected from donors infected in the previous wave of the epidemic [65].…”