Table_2_Dynamics of Viral Infection and Evolution of SARS-CoV-2 Variants in the Calabria Area of Southern Italy.XLSX

In this study, we report on the results of SARS-CoV-2 surveillance performed in an area of Southern Italy for 12 months (from March 2021 to February 2022). To this study, we have sequenced RNA from 609 isolates. We have identified circulating VOCs by Sanger sequencing of the S gene and defined their genotypes by whole-genome NGS sequencing of 157 representative isolates. Our results indicated that B.1 and Alpha were the only circulating lineages in Calabria in March 2021; while Alpha remained the most common variant between April 2021 and May 2021 (90 and 73%, respectively), we observed a concomitant decrease in B.1 cases and appearance of Gamma cases (6 and 21%, respectively); C.36.3 and Delta appeared in June 2021 (6 and 3%, respectively); Delta became dominant in July 2021 while Alpha continued to reduce (46 and 48%, respectively). In August 2021, Delta became the only circulating variant until the end of December 2021. As of January 2022, Omicron emerged and took over Delta (72 and 28%, respectively). No patient carrying Beta, Iota, Mu, or Eta variants was identified in this survey. Among the genomes identified in this study, some were distributed all over Europe (B1_S477N, Alpha_L5F, Delta_T95, Delta_G181V, and Delta_A222V), some were distributed in the majority of Italian regions (B1_S477N, B1_Q675H, Delta_T95I and Delta_A222V), and some were present mainly in Calabria (B1_S477N_T29I, B1_S477N_T29I_E484Q, Alpha_A67S, Alpha_A701S, and Alpha_T724I). Prediction analysis of the effects of mutations on the immune response (i.e., binding to class I MHC and/or recognition of T cells) indicated that T29I in B.1 variant; A701S in Alpha variant; and T19R in Delta variant were predicted to impair binding to class I MHC whereas the mutations A67S identified in Alpha; E484K identified in Gamma; and E156G and ΔF157/R158 identified in Delta were predicted to impair recognition by T cells. In conclusion, we report on the results of SARS-CoV-2 surveillance in Regione Calabria in the period between March 2021 and February 2022, identified variants that were enriched mainly in Calabria, and predicted the effects of identified mutations on host immune response.

本研究报告了2021年3月至2022年2月期间，在意大利南部某区域开展的为期12个月的新型冠状病毒（SARS-CoV-2）监测结果。本研究对609株分离株的RNA进行了测序：通过S基因的桑格测序（Sanger sequencing）鉴定了流行的关切变异株（Variants of Concern，VOCs），并通过对157株代表性分离株的全基因组下一代测序（Next-Generation Sequencing，NGS）明确了其基因型。研究结果显示，2021年3月时卡拉布里亚大区仅存在B.1和Alpha两种流行谱系；2021年4月至5月期间，Alpha仍为最常见变异株（占比分别为90%和73%），与此同时B.1病例占比下降，Gamma病例开始出现（占比分别为6%和21%）；C.36.3与Delta于2021年6月出现（占比分别为6%和3%）；2021年7月Delta成为优势变异株，Alpha占比持续下降（占比分别为46%和48%）。2021年8月至2021年12月末，Delta成为唯一的流行变异株。2022年1月，Omicron出现并取代Delta（占比分别为72%和28%）。本次监测未发现携带Beta、Iota、Mu或Eta变异株的感染者。本研究鉴定的基因组中，部分突变株在全欧洲范围内传播（如B1_S477N、Alpha_L5F、Delta_T95、Delta_G181V及Delta_A222V），部分在意大利多数大区流行（如B1_S477N、B1_Q675H、Delta_T95I及Delta_A222V），还有部分仅主要在卡拉布里亚大区出现（如B1_S477N_T29I、B1_S477N_T29I_E484Q、Alpha_A67S、Alpha_A701S及Alpha_T724I）。针对突变对免疫应答的影响（即与主要组织相容性复合体（Major Histocompatibility Complex，MHC）I类分子结合及/或T细胞识别）进行的预测分析显示：B.1变异株的T29I突变、Alpha变异株的A701S突变以及Delta变异株的T19R突变，均可能削弱其与MHC I类分子的结合能力；而Alpha变异株的A67S突变、Gamma变异株的E484K突变，以及Delta变异株的E156G和ΔF157/R158突变，则可能损害T细胞对其的识别能力。综上，本研究报告了2021年3月至2022年2月期间在卡拉布里亚大区开展的SARS-CoV-2监测结果，鉴定出主要在该区域富集的变异株，并预测了所鉴定突变对宿主免疫应答的影响。