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Intrinsic generation time of the SARS-CoV-2 Omicron variant: An observational study of household transmission.
Manica, Mattia; De Bellis, Alfredo; Guzzetta, Giorgio; Mancuso, Pamela; Vicentini, Massimo; Venturelli, Francesco; Zerbini, Alessandro; Bisaccia, Eufemia; Litvinova, Maria; Menegale, Francesco; Molina Grané, Carla; Poletti, Piero; Marziano, Valentina; Zardini, Agnese; d'Andrea, Valeria; Trentini, Filippo; Bella, Antonino; Riccardo, Flavia; Pezzotti, Patrizio; Ajelli, Marco; Giorgi Rossi, Paolo; Merler, Stefano.
  • Manica M; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • De Bellis A; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Guzzetta G; Department of Mathematics, University of Trento, Trento, Italy.
  • Mancuso P; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Vicentini M; Epidemiology Unit, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
  • Venturelli F; Epidemiology Unit, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
  • Zerbini A; Public Health Department, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
  • Bisaccia E; Unit of Clinical Immunology, Allergy and Advanced Biotechnologies, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Italy.
  • Litvinova M; Public Health Department, Azienda Unità Sanitaria Locale - IRCCS di Reggio Emilia, Reggio Emilia, Italy.
  • Menegale F; Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA.
  • Molina Grané C; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Poletti P; Department of Mathematics, University of Trento, Trento, Italy.
  • Marziano V; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Zardini A; Department of Mathematics, University of Trento, Trento, Italy.
  • d'Andrea V; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Trentini F; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Bella A; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Riccardo F; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Pezzotti P; Center for Health Emergencies, Fondazione Bruno Kessler, Trento, Italy.
  • Ajelli M; Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy.
  • Giorgi Rossi P; Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Rome, Italy.
  • Merler S; Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, Rome, Italy.
Lancet Reg Health Eur ; 19: 100446, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1914781
ABSTRACT

Background:

Starting from the final months of 2021, the SARS-CoV-2 Omicron variant expanded globally, swiftly replacing Delta, the variant that was dominant at the time. Many uncertainties remain about the epidemiology of Omicron; here, we aim to estimate its generation time.

Methods:

We used a Bayesian approach to analyze 23,122 SARS-CoV-2 infected individuals clustered in 8903 households as determined from contact tracing operations in Reggio Emilia, Italy, throughout January 2022. We estimated the distribution of the intrinsic generation time (the time between the infection dates of an infector and its secondary cases in a fully susceptible population), realized household generation time, realized serial interval (time between symptom onset of an infector and its secondary cases), and contribution of pre-symptomatic transmission.

Findings:

We estimated a mean intrinsic generation time of 6.84 days (95% credible intervals, CrI, 5.72-8.60), and a mean realized household generation time of 3.59 days (95%CrI 3.55-3.60). The household serial interval was 2.38 days (95%CrI 2.30-2.47) with about 51% (95%CrI 45-56%) of infections caused by symptomatic individuals being generated before symptom onset.

Interpretation:

These results indicate that the intrinsic generation time of the SARS-CoV-2 Omicron variant might not have shortened as compared to previous estimates on ancestral lineages, Alpha and Delta, in the same geographic setting. Like for previous lineages, pre-symptomatic transmission appears to play a key role for Omicron transmission. Estimates in this study may be useful to design quarantine, isolation and contact tracing protocols and to support surveillance (e.g., for the accurate computation of reproduction numbers).

Funding:

The study was partially funded by EU grant 874850 MOOD.
Keywords

Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal: Lancet Reg Health Eur Year: 2022 Document Type: Article Affiliation country: J.lanepe.2022.100446

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Full text: Available Collection: International databases Database: MEDLINE Topics: Variants Language: English Journal: Lancet Reg Health Eur Year: 2022 Document Type: Article Affiliation country: J.lanepe.2022.100446