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\begin{document}

\title{Genomic epidemiology of the main SARS-CoV-2 variants circulating in
Italy in 2020 and 2022 period}



\author[1]{Annalisa Bergna}%
\author[1]{A. Lai}%
\author[1]{Carla Della Ventura}%
\author[2]{Bianca Bruzzone}%
\author[3]{Alessandro Weisz}%
\author[4]{Morena d'Avenia}%
\author[5]{Sophie Testa}%
\author[6]{Carlo Torti}%
\author[7]{Caterina Sagnelli}%
\author[8]{Angela Menchise}%
\author[9]{Gaetano Brindicci}%
\author[10]{Daniela Francisci}%
\author[11]{Ilaria Vicenti}%
\author[12]{Nicola Clementi}%
\author[13]{Annapaola Callegaro}%
\author[14]{Emmanuele Venanzi Rullo}%
\author[15]{Sara Caucci}%
\author[2]{Vanessa De Pace}%
\author[2]{Andrea Orsi}%
\author[16]{Stefano Brusa}%
\author[17]{Francesca Greco}%
\author[18]{Vittoria Letizia}%
\author[19]{Emilia Vaccaro}%
\author[3]{Gianluigi Franci}%
\author[3]{Francesca Rizzo}%
\author[5]{Fabio Sagradi}%
\author[5]{Leonardo Lanfranchi}%
\author[7]{Nicola Coppola}%
\author[9]{Annalisa saracino}%
\author[20]{Michela Sampaolo}%
\author[21]{Silvia Ronchiadin}%
\author[1]{Massimo Galli}%
\author[1]{Agostino Riva}%
\author[1]{Gianguglielmo Zehender}%
\affil[1]{University of Milan}%
\affil[2]{IRCCS AOU San Martino-IST}%
\affil[3]{Universita degli Studi di Salerno Dipartimento di Medicina Chirurgia e Odontoiatria Scuola Medica Salernitana}%
\affil[4]{ASL Bari}%
\affil[5]{Azienda Socio Sanitaria Territoriale di Cremona}%
\affil[6]{Universita degli Studi Magna Graecia di Catanzaro Dipartimento di Scienze Mediche e Chirurgiche}%
\affil[7]{University of Campania "Luigi Vanvitelli}%
\affil[8]{AOR San Carlo Potenza}%
\affil[9]{University of Bari}%
\affil[10]{Santa Maria della Misericordia" Hospital}%
\affil[11]{Universita degli Studi di Siena Dipartimento di Biotecnologie Mediche}%
\affil[12]{Università "Vita-Salute" San Raffaele}%
\affil[13]{Department of Infectious Diseases}%
\affil[14]{University of Messina}%
\affil[15]{Universita Politecnica delle Marche Dipartimento di Scienze Biomediche e Sanita Pubblica}%
\affil[16]{Universita degli Studi di Napoli Federico II Dipartimento di Scienze Mediche Traslazionali}%
\affil[17]{UOC Microbiology and Virology}%
\affil[18]{AORN Sant’Anna and San Sebastiano di Caserta}%
\affil[19]{AOU ‘S Giovanni di Dio e Ruggi d'Aragona’ Università di Salerno}%
\affil[20]{IRCCS Ospedale San Raffaele}%
\affil[21]{Intesa Sanpaolo Innovation Center}%


\vspace{-1em}



  
  \date{May 24, 2024}


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\selectlanguage{english}
\begin{abstract}
Since the beginning of the pandemic, SARS-CoV-2 has shown a great
genomic variability, resulting in the continuous emergence of new
variants that has made their global monitoring and study a priority.
This work aimed to study the genomic heterogeneity, the temporal origin,
the rate of viral evolution and the population dynamics of the main
circulating variants (20E.EU1, Alpha and Delta) in Italy, in August
2020-January 2022 period. For phylogenetic analyses, two datasets were
evaluated for each variant, the former comprising international genomes
and the latter focusing on clusters containing at least 70\% of Italian
sequences. The international dataset showed 26 (23\% Italians, 23\%
singleton, 54\% mixed), 40 (60\% mixed, 37.5\% Italians, 1 singleton)
and 42 (85.7\% mixed, 9.5\% singleton, 4.8\% Italians) clusters with at
least one Italian sequence, in 20E.EU1 clade, Alpha and Delta variants,
respectively. International clusters presented tMRCAs between
13/06/2020-27/07/2021. R \textsubscript{e} values showed the highest
level between May-June until autumn 2020 in 20E.EU1 clade. The Alpha
variant showed an increase in the R \textsubscript{e} in December 2020,
when the highest mean value was estimated. Delta variant presented two
peaks: the first between March-May, and the second between June-July
2021. The present work highlighted a different evolutionary dynamic of
studied lineages with a high concordance between epidemiological
parameters estimation and phylodynamic trends suggesting that the
mechanism of replacement of the SARS-CoV-2 variants must be related to a
complex of factors involving the transmissibility, as well as the
implementation of control measures, and the level of cross-immunization
within the population.%
\end{abstract}%



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