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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.


We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility.


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.


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.


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.


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  1. Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021;372(6538):eabg3055.  https://doi.org/10.1126/science.abg3055  PMID: 33658326 
  2. Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature. 2021;593(7858):266-9.  https://doi.org/10.1038/s41586-021-03470-x  PMID: 33767447 
  3. European Centre for Disease Prevention and Control (ECDC). SARS-CoV-2 - increased circulation of variants of concern and vaccine rollout in the EU/EEA, 14th update. Risk assessment. Stockholm: ECDC; 2021. Available from: https://www.ecdc.europa.eu/en/publications-data/covid-19-risk-assessment-variants-vaccine-fourteenth-update-february-2021
  4. Galloway SE, Paul P, MacCannell DR, Johansson MA, Brooks JT, MacNeil A, et al. Emergence of SARS-CoV-2 B.1.1.7 lineage - United States, December 29, 2020-January 12, 2021. MMWR Morb Mortal Wkly Rep. 2021;70(3):95-9.  https://doi.org/10.15585/mmwr.mm7003e2  PMID: 33476315 
  5. Claro IM, da Silva Sales FC, Ramundo MS, Candido DS, Silva CAM, de Jesus JG, et al. Local transmission of SARS-CoV-2 lineage B.1.1.7, Brazil, December 2020. Emerg Infect Dis. 2021;27(3):970-2.  https://doi.org/10.3201/eid2703.210038  PMID: 33496249 
  6. Pango Lineages. Summary of B.1.1.7 data. Oxford: Pango network. [Accessed: 17 Jan 2022]. Available from: https://cov-lineages.org/global_report_B.1.1.7.html
  7. National Institute of Infectious Diseases (NIID). Brief report: New variant strain of SARS-CoV-2 Identified in travelers from Brazil. Tokyo; NIID;2021. Available from: https://www.niid.go.jp/niid/en/2019-ncov-e/10108-covid19-33-en.html
  8. Faria NR, Claro IM, Candido D, Moyses Franco LA, Andrade PS, Coletti TM, et al. Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings. Virological. 2021. Available from: https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
  9. Buss LF, Prete CA Jr, Abrahim CMM, Mendrone A Jr, Salomon T, de Almeida-Neto C, et al. Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic. Science. 2021;371(6526):288-92.  https://doi.org/10.1126/science.abe9728  PMID: 33293339 
  10. Sabino EC, Buss LF, Carvalho MPS, Prete CA Jr, Crispim MAE, Fraiji NA, et al. Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence. Lancet. 2021;397(10273):452-5.  https://doi.org/10.1016/S0140-6736(21)00183-5  PMID: 33515491 
  11. Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;592(7854):438-43.  https://doi.org/10.1038/s41586-021-03402-9  PMID: 33690265 
  12. Gaymard A, Bosetti P, Feri A, Destras G, Enouf V, Andronico A, et al. Early assessment of diffusion and possible expansion of SARS-CoV-2 lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021. Euro Surveill. 2021;26(9):2100133.  https://doi.org/10.2807/1560-7917.ES.2021.26.9.2100133  PMID: 33663644 
  13. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021;184(11):2939-2954.e9.  https://doi.org/10.1016/j.cell.2021.03.055  PMID: 33852911 
  14. Chen RE, Zhang X, Case JB, Winkler ES, Liu Y, VanBlargan LA, et al. Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies. Nat Med. 2021;27(4):717-26.  https://doi.org/10.1038/s41591-021-01294-w  PMID: 33664494 
  15. Wang P, Nair MS, Liu L, Iketani S, Luo Y, Guo Y, et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature. 2021;593(7857):130-5.  https://doi.org/10.1038/s41586-021-03398-2  PMID: 33684923 
  16. Supasa P, Zhou D, Dejnirattisai W, Liu C, Mentzer AJ, Ginn HM, et al. Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera. Cell. 2021;184(8):2201-2211.e7.  https://doi.org/10.1016/j.cell.2021.02.033  PMID: 33743891 
  17. Hoffmann M, Arora P, Groß R, Seidel A, Hörnich BF, Hahn AS, et al. SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies. Cell. 2021;184(9):2384-2393.e12.  https://doi.org/10.1016/j.cell.2021.03.036  PMID: 33794143 
  18. Nonaka CKV, Franco MM, Gräf T, de Lorenzo Barcia CA, de Ávila Mendonça RN, de Sousa KAF, et al. Genomic evidence of SARS-CoV-2 reinfection involving E484K spike mutation, Brazil. Emerg Infect Dis. 2021;27(5):1522-4.  https://doi.org/10.3201/eid2705.210191  PMID: 33605869 
  19. Naveca F, da Costa C, Nascimento V, Souza A, Corado A, Nascimento F, et al. SARS-CoV-2 reinfection by the new variant of concern (VOC) P.1 in Amazonas, Brazil. Virological. 2021. Available from: https://virological.org/t/sars-cov-2-reinfection-by-the-new-variant-of-concern-voc-p-1-in-amazonas-brazil/596
  20. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021;372(6544):815-21.  https://doi.org/10.1126/science.abh2644  PMID: 33853970 
  21. Zucman N, Uhel F, Descamps D, Roux D, Ricard JD. Severe reinfection with South African African severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant 501Y.V2. Clin Infect Dis. 2021;73(10):1945-6.  https://doi.org/10.1093/cid/ciab129  PMID: 33566076 
  22. Horby P, Bell I, Breuer J, Cevik M, Challen R, Davies N, et al. Update note on B.1.1.7 severity. London: New and Emerging Respiratory Virus Threats Advisory Group; 2021. Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/961042/S1095_NERVTAG_update_note_on_B.1.1.7_severity_20210211.pdf
  23. Challen R, Brooks-Pollock E, Read JM, Dyson L, Tsaneva-Atanasova K, Danon L. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ. 2021;372:n579.  https://doi.org/10.1136/bmj.n579  PMID: 33687922 
  24. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 covid-19 vaccine against the B. 1.351 variant. N Engl J Med. 2021;384(20):1885-98.  https://doi.org/10.1056/NEJMoa2102214  PMID: 33725432 
  25. Zhou D, Dejnirattisai W, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera. Cell. 2021;184(9):2348-2361.e6.  https://doi.org/10.1016/j.cell.2021.02.037  PMID: 33730597 
  26. Dipartimento di Protezione Civile. COVID-19 Italia. [COVID-19 data Italy]. Data repository. Rome; Protezione Civile; 24 Feb 2020. Italian. Available from: https://github.com/pcm-dpc/COVID-19
  27. Istituto Superiore di Sanità (ISS). COVID-19 ISS OpenData. Rome: ISS; 24 Feb 2020. Italian. Available from: https://www.epicentro.iss.it/coronavirus/open-data/covid_19-iss.xlsx
  28. Riccardo F, Ajelli M, Andrianou XD, Bella A, Del Manso M, Fabiani M, et al. Epidemiological characteristics of COVID-19 cases and estimates of the reproductive numbers 1 month into the epidemic, Italy, 28 January to 31 March 2020. Euro Surveill. 2020;25(49):2000790.  https://doi.org/10.2807/1560-7917.ES.2020.25.49.2000790  PMID: 33303064 
  29. Ministero della Salute. Covid-19, il nuovo Dpcm del Governo. [Covid-19, the new Decree of the President of the Council of Ministers]. Rome: Ministero della Salute; 3 Mar 2021. Italian. Available from: https://www.salute.gov.it/portale/nuovocoronavirus/dettaglioNotizieNuovoCoronavirus.jsp?lingua=italiano&menu=notizie&p=dalministero&id=5354
  30. Manica M, Guzzetta G, Riccardo F, Valenti A, Poletti P, Marziano V, et al. Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy. Nat Commun. 2021;12(1):4570.  https://doi.org/10.1038/s41467-021-24832-z  PMID: 34315899 
  31. Istituto Superiore di Sanità. Prevalenza delle varianti VOC 202012/01 (lineage B.1.1.7), P.1, e 501.V2 (lineage B.1.351) in Italia. Indagine del 18 febbraio 2021. [Prevalence of VOC variants 202012/01 (lineage B.1.1.7), P1 and 501.V2 (lineage B.1.351) in Italy]. Rome: ISS; 2021. Italian. Available from: https://www.epicentro.iss.it/coronavirus/pdf/sars-cov-2-monitoraggio-varianti-indagini-rapide-18-febbraio-2021.pdf
  32. Istituto Superiore di Sanità. Prevalenza delle varianti VOC (Variant Of Concern) in Italia: lineage B.1.1.7, P.1, P.2, lineage B.1.351, lineage B.1.525 (Indagine del 18/3/2021). [Prevalence of VOC (variant of concern) variants in Italy: lineage B.1.1.7, P.1, P.2, lineage B.1.351, lineage B.1.525 (survey from 18/3/2021)]. Rome: ISS; 2021. Italian. Available from: https://www.epicentro.iss.it/coronavirus/pdf/sars-cov-2-monitoraggio-varianti-indagini-rapide-18-marzo-2021.pdf
  33. Ministero della Salute. Indagine rapida per la valutazione della prevalenza delle varianti VOC 202012/01 (ovvero lineage B.1.1.7-Regno Unito), P1 (ovvero Brasiliana), e 501.V2 (ovvero lineage B.135- Sud Africana) in Italia. [Rapid survey for the assessment of the prevalence of VOC variants 202012/01 (i.e. lineage B.1.1.7-United Kingdom), P1 (i.e. Brazilian), and 501.V2 (i.e. lineage B.135- South African) in Italy]. Rome: Ministero della Salute; 17 Feb 2021. Italian. Available from: https://www.trovanorme.salute.gov.it/norme/renderNormsanPdf?anno=2021&codLeg=78864&parte=1%20&serie=null
  34. Centers for Disease Control (CDC). SARS-CoV-2 variant classifications and definitions. Atlanta: CDC. [Accessed: 17 Jan 2022]. Available from: https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-info.html
  35. Cereda D, Manica M, Tirani M, Rovida F, Demicheli V, Ajelli M, et al. The early phase of the COVID-19 epidemic in Lombardy, Italy. Epidemics. 2021;37:100528.  https://doi.org/10.1016/j.epidem.2021.100528  PMID: 34814093 
  36. Zhao S, Lou J, Cao L, Zheng H, Chong MKC, Chen Z, et al. Quantifying the transmission advantage associated with N501Y substitution of SARS-CoV-2 in the UK: an early data-driven analysis. J Travel Med. 2021;28(2):taab011.  https://doi.org/10.1093/jtm/taab011  PMID: 33506254 
  37. Leung K, Shum MH, Leung GM, Lam TT, Wu JT. Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020. Euro Surveill. 2021;26(1):2002106.  https://doi.org/10.2807/1560-7917.ES.2020.26.1.2002106  PMID: 33413740 
  38. Kissler SM, Fauver JR, Mack C, Tai CG, Breban MI, Watkins AE, et al. Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated persons. N Engl J Med. 2021;385(26):2489-91.  https://doi.org/10.1056/NEJMc2102507  PMID: 34941024 
  39. Hu S, Wang W, Wang Y, Litvinova M, Luo K, Ren L, et al. Infectivity, susceptibility, and risk factors associated with SARS-CoV-2 transmission under intensive contact tracing in Hunan, China. Nat Commun. 2021;12(1):1533.  https://doi.org/10.1038/s41467-021-21710-6  PMID: 33750783 
  40. Brookman S, Cook J, Zucherman M, Broughton S, Harman K, Gupta A. Effect of the new SARS-CoV-2 variant B.1.1.7 on children and young people. Lancet Child Adolesc Health. 2021;5(4):e9-10.  https://doi.org/10.1016/S2352-4642(21)00030-4  PMID: 33581054 
  41. Walker AS, Vihta KD, Gethings O, Pritchard E, Jones J, House T, et al. Increased infections, but not viral burden, with a new SARS-CoV-2 variant. medRxiv2021.01.13.21249721. Preprint.  https://doi.org/10.1101/2021.01.13.21249721 
  42. Davies NG, Jarvis CI, Edmunds WJ, Jewell NP, Diaz-Ordaz K, Keogh RH. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature. 2021;593(7858):270-4. https://doi.org/10.1038/s41586-021-03426-1 
  43. Challen R, Brooks-Pollock E, Read JM, Dyson L, Tsaneva-Atanasova K, Danon L. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ. 2021;372(579):n579.  https://doi.org/10.1136/bmj.n579  PMID: 33687922 

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