Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021

Stefanelli, P.; Trentini, F.; Guzzetta, G.; Marziano, V.; Mammone, A.; Schepisi, M. S.; Poletti, P.; Grane, C. M.; Manica, M.; del Manso, M.; Andrianou, X.; Ajelli, M.; Rezza, G.; Brusaferro, S.; Merler, S.; Di Martino, A.; Ambrosio, L.; Lo Presti, A.; Fiore, S.; Fabiani, C.; Benedetti, E.; Di Mario, G.; Facchini, M.; Puzelli, S.; Calzoletti, L.; Fontana, S.; Venturi, G.; Fortuna, C.; Marsili, G.; Amendola, A.; Stuppia, L.; Savini, G.; Picerno, A.; Lopizzo, T.; Dell'Edera, D.; Minchella, P.; Greco, F.; Viglietto, G.; Atripaldi, L.; Limone, A.; D'Agaro, P.; Licastro, D.; Pongolini, S.; Sambri, V.; Dirani, G.; Zannoli, S.; Affanni, P.; Colucci, M. E.; Capobianchi, M. R.; Icardi, G.; Bruzzone, B.; Lillo, F.; Orsi, A.; Pariani, E.; Baldanti, F.; Molecolare, U. V.; Gismondo, M. R.; Maggi, F.; Caruso, A.; Ceriotti, F.; Boniotti, M. B.; Barbieri, I.; Bagnarelli, P.; Menzo, S.; Garofalo, S.; Scutella, M.; Pagani, E.; Collini, L.; Ghisetti, V.; Brossa, S.; Ru, G.; Bozzetta, E.; Chironna, M.; Parisi, A.; Rubino, S.; Serra, C.; Piras, G.; Coghe, F.; Vitale, F.; Tramuto, F.; Scalia, G.; Palermo, C. I.; Mancuso, G.; Pollicino, T.; Di Gaudio, F.; Vullo, S.; Reale, S.; Cusi, M. G.; Rossolini, G. M.; Pistello, M.; Mencacci, A.; Camilloni, B.; Severini, S.; Di Benedetto, M.; Terregino, C.; Monne, I.; Biscaro, V.

doi:10.2807/1560-7917.ES.2022.27.5.2100429

Background: Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains. Aim: We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility. Methods: We conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains. Results: The Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55–1.57 times the level of historical lineages (95% CrI: 1.45–1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03–1.23) with complete immune evasion to 1.39 (95% CrI: 1.26–1.56) for complete cross-protection. Conclusion: We assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility.

Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021 / Stefanelli, P.; Trentini, F.; Guzzetta, G.; Marziano, V.; Mammone, A.; Schepisi, M. S.; Poletti, P.; Grane, C. M.; Manica, M.; del Manso, M.; Andrianou, X.; Ajelli, M.; Rezza, G.; Brusaferro, S.; Merler, S.; Di Martino, A.; Ambrosio, L.; Lo Presti, A.; Fiore, S.; Fabiani, C.; Benedetti, E.; Di Mario, G.; Facchini, M.; Puzelli, S.; Calzoletti, L.; Fontana, S.; Venturi, G.; Fortuna, C.; Marsili, G.; Amendola, A.; Stuppia, L.; Savini, G.; Picerno, A.; Lopizzo, T.; Dell'Edera, D.; Minchella, P.; Greco, F.; Viglietto, G.; Atripaldi, L.; Limone, A.; D'Agaro, P.; Licastro, D.; Pongolini, S.; Sambri, V.; Dirani, G.; Zannoli, S.; Affanni, P.; Colucci, M. E.; Capobianchi, M. R.; Icardi, G.; Bruzzone, B.; Lillo, F.; Orsi, A.; Pariani, E.; Baldanti, F.; Molecolare, U. V.; Gismondo, M. R.; Maggi, F.; Caruso, A.; Ceriotti, F.; Boniotti, M. B.; Barbieri, I.; Bagnarelli, P.; Menzo, S.; Garofalo, S.; Scutella, M.; Pagani, E.; Collini, L.; Ghisetti, V.; Brossa, S.; Ru, G.; Bozzetta, E.; Chironna, M.; Parisi, A.; Rubino, S.; Serra, C.; Piras, G.; Coghe, F.; Vitale, F.; Tramuto, F.; Scalia, G.; Palermo, C. I.; Mancuso, G.; Pollicino, T.; Di Gaudio, F.; Vullo, S.; Reale, S.; Cusi, M. G.; Rossolini, G. M.; Pistello, M.; Mencacci, A.; Camilloni, B.; Severini, S.; Di Benedetto, M.; Terregino, C.; Monne, I.; Biscaro, V.. - In: EUROSURVEILLANCE. - ISSN 1025-496X. - 27:5(2022). [10.2807/1560-7917.ES.2022.27.5.2100429]