loading page

Genomic epidemiology of the main SARS-CoV-2 variants circulating in Italy in 2020 and 2022 period
  • +31
  • Annalisa Bergna,
  • A. Lai,
  • Carla Della Ventura,
  • Bianca Bruzzone,
  • Alessandro Weisz,
  • Morena d'Avenia,
  • Sophie Testa,
  • Carlo Torti,
  • Caterina Sagnelli,
  • Angela Menchise,
  • Gaetano Brindicci,
  • Daniela Francisci,
  • Ilaria Vicenti,
  • Nicola Clementi,
  • Annapaola Callegaro,
  • Emmanuele Venanzi Rullo,
  • Sara Caucci,
  • Vanessa De Pace,
  • Andrea Orsi,
  • Stefano Brusa,
  • Francesca Greco,
  • Vittoria Letizia,
  • Emilia Vaccaro,
  • Gianluigi Franci,
  • Francesca Rizzo,
  • Fabio Sagradi,
  • Leonardo Lanfranchi,
  • Nicola Coppola,
  • Annalisa saracino,
  • Michela Sampaolo,
  • Silvia Ronchiadin,
  • Massimo Galli,
  • Agostino Riva,
  • Gianguglielmo Zehender
Annalisa Bergna
University of Milan
Author Profile
A. Lai
University of Milan

Corresponding Author:alessia.lai@unimi.it

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

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 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 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.
14 Jul 2023Submitted to Journal of Medical Virology
14 Jul 2023Submission Checks Completed
14 Jul 2023Assigned to Editor
14 Jul 2023Review(s) Completed, Editorial Evaluation Pending
14 Jul 2023Reviewer(s) Assigned
05 Aug 2023Editorial Decision: Revise Major
22 Sep 20231st Revision Received
25 Sep 2023Submission Checks Completed
25 Sep 2023Assigned to Editor
25 Sep 2023Review(s) Completed, Editorial Evaluation Pending
25 Sep 2023Reviewer(s) Assigned
03 Oct 2023Editorial Decision: Revise Major