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. 2021 Apr 22;13(5):731.
doi: 10.3390/v13050731.

Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study

Loredana Capozzi  1 , Angelica Bianco  1 , Laura Del Sambro  1 , Domenico Simone  1 , Antonio Lippolis  2 , Maria Notarnicola  2 , Graziano Pesole  3 , Lorenzo Pace  1 , Domenico Galante  1 , Antonio Parisi  1
Affiliations

Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study

Loredana Capozzi et al. Viruses. .

Abstract

In order to provide insights into the evolutionary and epidemiological viral dynamics during the current COVID-19 pandemic in South Eastern Italy, a total of 298 genomes of SARS-CoV-2 strains collected in the Apulia and Basilicata regions, between March 2020 and January 2021, were sequenced. The genomic analysis performed on the draft genomes allowed us to assign the genetic clades and lineages of belonging to each sample and provide an overview of the main circulating viral variants. Our data showed the spread in Apulia and Basilicata of SARS-CoV-2 variants which have emerged during the second wave of infections and are being currently monitored worldwide for their increased transmission rate and their possible impact on vaccines and therapies. These results emphasize the importance of genome sequencing for the epidemiological surveillance of the new SARS-CoV-2 variants' spread.

Keywords: COVID-19; Nextstrain clade; Pangolin lineage; SARS-CoV-2; genomic surveillance; variants of concern; whole genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Pangolin lineages detected in Apulia and Basilicata regions, from March 2020 to January 2021.
Figure 2
Figure 2
Phylogenetic tree showing the relationship between the 2244 Italian SARS-Cov-2 genome sequences. The tree was inferred with the approximate maximum likelihood method as implemented by FastTree v2.1 [21] and decorated with iTOL. Nextstrain clades are highlighted in pastel colors. The Italian region of sample collection is shown across the inner colored strip, the outer circle displays the sampling date, sorted into first wave and second wave. A newick (plain text) version of the phylogenetic tree, with branch lengths and support values at nodes, is reported in Supplementary File 2.
Figure 3
Figure 3
(A): Distribution of Nextstrain Clades for 353 SARS-CoV-2 genome sequences collected from the Apulia and Basilicata regions from March 2020 to December 2020. (B). Distribution of Nextstrain Clades for 1946 SARS-CoV-2 genome sequences submitted to GISAID from Italy (not including Apulia and Basilicata regions) and collected from January 2020 to December 2020.
Figure 3
Figure 3
(A): Distribution of Nextstrain Clades for 353 SARS-CoV-2 genome sequences collected from the Apulia and Basilicata regions from March 2020 to December 2020. (B). Distribution of Nextstrain Clades for 1946 SARS-CoV-2 genome sequences submitted to GISAID from Italy (not including Apulia and Basilicata regions) and collected from January 2020 to December 2020.
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