Intrinsic generation time of the SARS-CoV-2 Omicron variant: an observational study of household transmission

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).Copyright (c) 2022 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/

Estimation of the incubation period and generation time of SARS-CoV-2 Alpha and Delta variants from contact tracing data

: Quantitative information on epidemiological quantities such as the incubation period and generation time of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is scarce. We analysed a dataset collected during contact tracing activities in the province of Reggio Emilia, Italy, throughout 2021. We determined the distributions of the incubation period for the Alpha and Delta variants using information on negative polymerase chain reaction tests and the date of last exposure from 282 symptomatic cases. We estimated the distributions of the intrinsic generation time using a Bayesian inference approach applied to 9724 SARS-CoV-2 cases clustered in 3545 households where at least one secondary case was recorded. We estimated a mean incubation period of 4.9 days (95% credible intervals, CrI, 4.4-5.4) for Alpha and 4.5 days (95% CrI 4.0-5.0) for Delta. The intrinsic generation time was estimated to have a mean of 7.12 days (95% CrI 6.27-8.44) for Alpha and of 6.52 days (95% CrI 5.54-8.43) for Delta. The household serial interval was 2.43 days (95% CrI 2.29-2.58) for Alpha and 2.74 days (95% CrI 2.62-2.88) for Delta, and the estimated proportion of pre-symptomatic transmission was 48-51% for both variants. These results indicate limited differences in the incubation period and intrinsic generation time of SARS-CoV-2 variants Alpha and Delta compared to ancestral lineages

The impact of chest CT body composition parameters on clinical outcomes in COVID-19 patients

We assessed the impact of chest CT body composition parameters on outcomes and disease severity at hospital presentation of COVID-19 patients, focusing also on the possible mediation of body composition in the relationship between age and death in these patients. Chest CT scans performed at hospital presentation by consecutive COVID-19 patients (02/27/2020-03/13/2020) were retrospectively reviewed to obtain pectoralis muscle density and total, visceral, and intermuscular adipose tissue areas (TAT, VAT, IMAT) at the level of T7-T8 vertebrae. Primary outcomes were: hospitalization, mechanical ventilation (MV) and/or death, death alone. Secondary outcomes were: C-reactive protein (CRP), oxygen saturation (SO2), CT disease extension at hospital presentation. The mediation of body composition in the effect of age on death was explored. Of the 318 patients included in the study (median age 65.7 years, females 37.7%), 205 (64.5%) were hospitalized, 68 (21.4%) needed MV, and 58 (18.2%) died. Increased muscle density was a protective factor while increased TAT, VAT, and IMAT were risk factors for hospitalization and MV/death. All these parameters except TAT had borderline effects on death alone. All parameters were associated with SO2 and extension of lung parenchymal involvement at CT; VAT was associated with CRP. Approximately 3% of the effect of age on death was mediated by decreased muscle density. In conclusion, low muscle quality and ectopic fat accumulation were associated with COVID-19 outcomes, VAT was associated with baseline inflammation. Low muscle quality partly mediated the effect of age on mortality.We assessed the impact of chest CT body composition parameters on outcomes and disease severity at hospital presentation of COVID-19 patients, focusing also on the possible mediation of body composition in the relationship between age and death in these patients. Chest CT scans performed at hospital presentation by consecutive COVID-19 patients (02/ 27/2020-03/13/2020) were retrospectively reviewed to obtain pectoralis muscle density and total, visceral, and intermuscular adipose tissue areas (TAT, VAT, IMAT) at the level of T7-T8 vertebrae. Primary outcomes were: hospitalization, mechanical ventilation (MV) and/or death, death alone. Secondary outcomes were: C-reactive protein (CRP), oxygen saturation (SO2), CT disease extension at hospital presentation. The mediation of body composition in the effect of age on death was explored. Of the 318 patients included in the study (median age 65.7 years, females 37.7%), 205 (64.5%) were hospitalized, 68 (21.4%) needed MV, and 58 (18.2%) died. Increased muscle density was a protective factor while increased TAT, VAT, and IMAT were risk factors for hospitalization and MV/death. All these parameters except TAT had borderline effects on death alone. All parameters were associated with SO2 and extension of lung parenchymal involvement at CT; VAT was associated with CRP. Approximately 3% of the effect of age on death was mediated by decreased muscle density. In conclusion, low muscle quality and ectopic fat accumulation were associated with COVID-19 outcomes, VAT was associated with baseline inflammation. Low muscle quality partly mediated the effect of age on mortality

Association between Exposure to Influenza Vaccination and COVID-19 Diagnosis and Outcomes

We explored whether influenza vaccination (IV) affects susceptibility to SARS-CoV-2 infection and clinical outcomes in COVID-19 patients in 17,608 residents of the Italian province of Reggio Emilia undergoing a SARS-CoV-2 test. Exposure to IV was ascertained and the strength of the association with SARS-CoV-2 positivity expressed with odds ratios (OR). Rates of hospitalisations and death in those found positive were assessed and hazard ratios (HR) were estimated. The prevalence of IV was 34.3% in the 4885 SARS-CoV-2 positive and 29.5% in the 12,723 negative subjects, but the adjusted OR indicated that vaccinated individuals had a lower probability of testing positive (OR = 0.89; 95% CI 0.80–0.99). Among the 4885 positive individuals, 1676 had received IV. After adjusting for confounding factors, there was no association between IV and hospitalisation (1.00; 95% CI 0.84–1.29) or death (HR = 1.14; 95% CI 0.95–1.37). However, for patients age ≥65 vaccinated close to the SARS-CoV-2 outbreak, HRs were 0.66 (95% CI: 0.44–0.98) and 0.70 (95% CI 0.50–1.00), for hospitalisation and death, respectively. In this study, IV was associated with a lower probability of COVID-19 diagnosis. In COVID-19 patients, overall, IV did not affect outcomes, although a protective effect was observed for the elderly receiving IV almost in parallel with the SARS-CoV-2 outbreak. These findings provide reassurance in planning IV campaigns and underscore the need for exploring further their impact on COVID-19

Sorveglianza delle infezioni ospedaliere nell’Unità di Rianimazione dell’Azienda Ospedaliera-Universitaria Policlinico di Modena

Nell’Unità di Rianimazione dell’Azienda Ospedaliero-Universitaria Policlinico di Modena è stato applicato un sistema di sorveglianza delle infezioni ospedaliere (IOS) denominato SPIN-UTI (Sorveglianza Prospettica delle Infezioni Nosocomiali nelle Unita di Terapia Intensiva), un sistema di rilevazione utilizzato in diverse terapie intensive italiane, costruito e messo punto utilizzando la metodologia dal network europeo di sorveglianza delle infezioni HELICSICU, con l’obiettivo di consentire valutazioni e confronti sul fenomeno estesi ed affidabili sia a livello nazionale che internazionale.La sorveglianza, di tipo prospettico e patient-based, è durata per 6 mesi (ottobre 2010-marzo 2011): tutti i pazienti ricoverati in TerapiaIntensiva per più di 48h sono stati monitorati per tutto il tempo del ricovero e le IOS sorvegliate sono state le polmoniti nosocomiali; le infezioni del torrente ematico; le infezioni associate a cateteri intravascolari centrali; le infezioni delle vie urinarie. 70 pazienti (51% maschi) con una età media pari a 74 anni (± 15) sono stati ospitati per più di 48 ore prevalentemente (91%) per un ricovero di tipo medico. Durante la sorveglianza sono state registrate 24 infezioni in 15 soggetti: l’incidenza cumulativa di soggetti con infezione potenzialmente correlata alla attività assistenziale risulta così pari al 21.4%, mentre la densità di incidenza pari a 23.7 infezioni ogni 1000 giornate di degenza. Le infezioni più diffuse sono risultate le polmoniti (16 episodi pari al 67% delle infezioni registrate) seguite da quelle delle vie urinarie (6 episodi- 25%). La durata della degenza in rianimazione (34 vs 9 giorni) così come la mortalità ospedaliera (67% vs 26%) appaiono significativamente più elevate per i pazienti con IOS rispetto a quelle registrate per i soggetti privi di infezioni.I dati rilevati risultano in linea con quanto osservato nello stesso periodo nelle altre TI italiane aderenti al sistema di sorveglianza SPINUTI

Incidence and Characteristics of Adverse Events after COVID-19 Vaccination in a Population-Based Programme

Compliance with vaccination is linked to its safety. In Italy, a plan to identify people who could be at an increased risk of adverse events (AEs) was defined so they could be vaccinated in a protected setting. We conducted an audit to describe the process of AE risk assessment and occurrence in the Reggio Emilia Province in Italy in people who received any of the four COVID-19 vaccines currently used in Italy. Incidence of AEs was calculated by dose and type of vaccine and type of setting (standard vs. protected). After 182,056 first doses were administered, 521 (0.3%) AEs were reported. Most of the AEs were non-serious (91.4%) and non-allergic (92.7%). The percentage of AEs was similar in both settings: 0.3% in the standard setting and 0.2% in the protected setting. However, the incidence of AEs was higher among those who had an allergist visit than among those who did not (IR 666.7 vs. 124.9). All deaths (1.6/100.000) occurred in standard settings and after the Pfizer and Moderna vaccines. The incidence of AEs was lower after the second dose (IR 286.2 vs. 190.3), except for mRNA vaccines, for which it was higher after the second dose (IR 169.8 vs. 251.8). Although vaccination in a protected medical setting could reassure patients with a history of allergies to be vaccinated, allergy history and other anamnestic information is not useful in predicting the risk of COVID-19 vaccine-related AEs in the general population

Effect of an enhanced public health contact tracing intervention on the secondary transmission of SARS-CoV-2 in educational settings: The four-way decomposition analysis

Background: The aim of our study was to test the hypothesis that the community contact tracing strategy of testing contacts in households immediately instead of at the end of quarantine had an impact on the transmission of SARS-CoV-2 in schools in Reggio Emilia Province. Methods: We analysed surveillance data on notification of COVID-19 cases in schools between 1 September 2020 and 4 April 2021. We have applied a mediation analysis that allows for interaction between the intervention (before/after period) and the mediator. Results: Median tracing delay decreased from 7 to 3.1 days and the percentage of the known infection source increased from 34–54.8% (incident rate ratio-IRR 1.61 1.40–1.86). Implementation of prompt contact tracing was associated with a 10% decrease in the number of secondary cases (excess relative risk –0.1 95% CI –0.35–0.15). Knowing the source of infection of the index case led to a decrease in secondary transmission (IRR 0.75 95% CI 0.63–0.91) while the decrease in tracing delay was associated with decreased risk of secondary cases (1/IRR 0.97 95% CI 0.94–1.01 per one day of delay). The direct effect of the intervention accounted for the 29% decrease in the number of secondary cases (excess relative risk –0.29 95%–0.61 to 0.03). Conclusions: Prompt contact testing in the community reduces the time of contact tracing and increases the ability to identify the source of infection in school outbreaks. Although there are strong reasons for thinking it is a causal link, observed differences can be also due to differences in the force of infection and to other control measures put in place. Funding: This project was carried out with the technical and financial support of the Italian Ministry of Health – CCM 2020 and Ricerca Corrente Annual Program 2023

Intrinsic generation time of the SARS-CoV-2 Omicron variant: An observational study of household transmission

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