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Intrinsic Generation Time of the SARS-CoV-2 Omicron Variant: An Observational Study of Household Transmission

20 Pages Posted: 28 Mar 2022

See all articles by Mattia Manica

Mattia Manica

Fondazione Bruno Kessler - Center for Health Emergencies

Alfredo De Bellis

Fondazione Bruno Kessler

Giorgio Guzzetta

Fondazione Bruno Kessler

Pamela Mancuso

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit

Massimo Vicentini

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit

Francesco Venturelli

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit

Eufemia Bisaccia

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Public Health Service

Maria Litvinova

affiliation not provided to SSRN

Piero Poletti

Fondazione Bruno Kessler

Valentina Marziano

Fondazione Bruno Kessler

Agnese Zardini

Fondazione Bruno Kessler

Valeria d'Andrea

Fondazione Bruno Kessler

Filippo Trentini

affiliation not provided to SSRN

Antonino Bella

Istituto Superiore di Sanità

Flavia Riccardo

Istituto Superiore di Sanità

Patrizio Pezzotti

Istituto Superiore di Sanità - Dipartimento Malattie Infettive

Marco Ajelli

Indiana University

Paolo Giorgi Rossi

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit

Stefano Merler

Fondazione Bruno Kessler - Center for Information Technology

More...

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, and it is yet to be established whether its generation time is shorter than that of previous variants.

Method: We used a Bayesian approach to analyze 23,122 SARS-CoV-2 infected individuals clustered in 8,903 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, and contribution of pre-symptomatic transmission.

Results: We estimated a mean intrinsic generation time of 6.84 days (95% 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 limited differences between the intrinsic generation time of the SARS-CoV-2 Omicron variant as compared to previous estimates on ancestral lineages, Alpha and Delta. Like for previous lineages, pre-symptomatic transmission appears to play a key role for Omicron transmission.

Funding Information: MM, AZ, FR, PPe, GG, and SM acknowledge funding from EU grant 874850 MOOD (catalogued as MOOD 000).

Declaration of Interests: MA has received research funding from Seqirus. The funding is not related to COVID-19. All other authors declare no competing interest.

Ethics Approval Statement: Covid-19 surveillance data collection, including specific studies on contact tracing, was authorized by the Italian Presidency of the Council of Ministers on 27 February 2020 (ordinance No 640, article 1 [15]).

Keywords: generation time, Omicron, SARS-CoV-2, COVID-19, Bayesian inference, contact tracing

Suggested Citation

Manica, Mattia and De Bellis, Alfredo and Guzzetta, Giorgio and Mancuso, Pamela and Vicentini, Massimo and Venturelli, Francesco and Bisaccia, Eufemia and Litvinova, Maria and Poletti, Piero and Marziano, Valentina and Zardini, Agnese and d'Andrea, Valeria and Trentini, Filippo and Bella, Antonino and Riccardo, Flavia and Pezzotti, Patrizio and Ajelli, Marco and Rossi, Paolo Giorgi and Merler, Stefano, Intrinsic Generation Time of the SARS-CoV-2 Omicron Variant: An Observational Study of Household Transmission. Available at SSRN: https://ssrn.com/abstract=4068368 or http://dx.doi.org/10.2139/ssrn.4068368

Mattia Manica

Fondazione Bruno Kessler - Center for Health Emergencies ( email )

Trento
Italy

Alfredo De Bellis

Fondazione Bruno Kessler ( email )

Via Sommarive 18
Povo
Trento, 38123
Italy

Giorgio Guzzetta

Fondazione Bruno Kessler ( email )

Via Sommarive 18
Povo
Trento, 38123
Italy

Pamela Mancuso

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit ( email )

Massimo Vicentini

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit ( email )

Francesco Venturelli

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit ( email )

Italy
+390522335499 (Phone)

Eufemia Bisaccia

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Public Health Service ( email )

Maria Litvinova

affiliation not provided to SSRN ( email )

No Address Available

Piero Poletti

Fondazione Bruno Kessler ( email )

Via Sommarive 18
Povo
Trento, 38123
Italy

Valentina Marziano

Fondazione Bruno Kessler ( email )

Via Sommarive 18
Povo
Trento, 38123
Italy

Agnese Zardini

Fondazione Bruno Kessler ( email )

Via Sommarive 18
Povo
Trento, 38123
Italy

Valeria D'Andrea

Fondazione Bruno Kessler ( email )

Filippo Trentini

affiliation not provided to SSRN ( email )

No Address Available

Antonino Bella

Istituto Superiore di Sanità ( email )

Viale Regina Elena 299
Roma, 00161
Italy

Flavia Riccardo

Istituto Superiore di Sanità ( email )

Viale Regina Elena 299
Roma, 00161
Italy

Patrizio Pezzotti

Istituto Superiore di Sanità - Dipartimento Malattie Infettive ( email )

Italy

Marco Ajelli

Indiana University ( email )

Paolo Giorgi Rossi

Azienda Unità Sanitaria Locale (AUSL) - IRCCS di Reggio Emilia - Epidemiology Unit ( email )

Italy

Stefano Merler (Contact Author)

Fondazione Bruno Kessler - Center for Information Technology ( email )

Via Sommarive 18
Povo
Trento, 38123
Italy

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