De Marco Carmela, Veneziano Claudia, Massacci Alice, Pallocca Matteo, Marascio Nadia, Quirino Angela, Barreca Giorgio Settimo, Giancotti Aida, Gallo Luigia, Lamberti Angelo Giuseppe, Quaresima Barbara, Santamaria Gianluca, Biamonte Flavia, Scicchitano Stefania, Trecarichi Enrico Maria, Russo Alessandro, Torella Daniele, Quattrone Aldo, Torti Carlo, Matera Giovanni, De Filippo Caterina, Costanzo Francesco Saverio, Viglietto Giuseppe
Department of Experimental and Clinical Medicine, "Magna Graecia" University, Catanzaro, Italy.
Interdepartmental Center of Services, Molecular Genomics and Pathology, "Magna Graecia" University, Catanzaro, Italy.
Front Microbiol. 2022 Jul 28;13:934993. doi: 10.3389/fmicb.2022.934993. eCollection 2022.
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.
在本研究中，我们报告了在意大利南部某地区进行的为期12个月（从2021年3月至2022年2月）的新冠病毒（SARS-CoV-2）监测结果。在这项研究中，我们对609株病毒分离株的RNA进行了测序。我们通过S基因的桑格测序确定了流行的变异株，并通过对157株代表性分离株进行全基因组二代测序确定了它们的基因型。我们的结果表明，B.1和阿尔法是2021年3月在卡拉布里亚仅有的流行谱系；虽然阿尔法在2021年4月至5月期间仍然是最常见的变异株（分别为90%和73%），但我们观察到B.1病例同时减少，伽马病例出现（分别为6%和21%）；C.36.3和德尔塔于2021年6月出现（分别为6%和3%）；德尔塔在2021年7月成为优势毒株，而阿尔法毒株继续减少（分别为46%和48%）。2021年8月，德尔塔成为唯一流行的变异株，直至2021年12月底。截至2022年1月，奥密克戎出现并取代了德尔塔（分别为72%和28%）。在本次调查中未发现携带贝塔、约塔、缪或埃塔变异株的患者。在本研究中鉴定出的基因组中，一些分布在欧洲各地（B1_S477N、阿尔法_L5F、德尔塔_T95、德尔塔_G181V和德尔塔_A222V），一些分布在意大利的大部分地区（B1_S477N、B1_Q675H、德尔塔_T95I和德尔塔_A222V），还有一些主要存在于卡拉布里亚（B1_S477N_T29I、B1_S477N_T29I_E484Q、阿尔法_A67S、阿尔法_A701S和阿尔法_T724I）。对突变对免疫反应的影响（即与I类主要组织相容性复合体结合和/或T细胞识别）的预测分析表明，B.1变异株中的T29I；阿尔法变异株中的A701S；以及德尔塔变异株中的T19R预计会损害与I类主要组织相容性复合体的结合，而在阿尔法中鉴定出的A67S突变；在伽马中鉴定出的E484K突变；以及在德尔塔中鉴定出的E156G和ΔF157/R158突变预计会损害T细胞的识别。总之，我们报告了2021年3月至2022年2月期间卡拉布里亚地区新冠病毒监测的结果，确定了主要在卡拉布里亚富集的变异株，并预测了已鉴定突变对宿主免疫反应的影响。
