Evaluating a SARS-CoV-2 screening strategy based on serological tests.

BACKGROUND: facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. Although RT-PCR is the most reliable technique to detect ongoing infections, serological tests are frequently proposed as tools in heterogeneous screening strategies. OBJECTIVES: to analyse the performance of a screening strategy proposed by the local government of Tuscany (Central Italy), which first uses qualitative rapid tests for antibody detection, and then RT-PCR tests on the positive subjects. METHODS: a simulation study is conducted to investigate the number of RT-PCR tests required by the screening strategy and the undetected ongoing infections in a pseudo-population of 500,000 subjects, under different prevalence scenarios and assuming a sensitivity of the serological test ranging from 0.50 to 0.80 (specificity 0.98). A compartmental model is used to predict the number of new infections generated by the false negatives two months after the screening, under different values of the infection reproduction number. RESULTS: assuming a sensitivity equal to 0.80 and a prevalence of 0.3%, the screening procedure would require on average 11,167 RT-PCR tests and would produce 300 false negatives, responsible after two months of a number of contagions ranging from 526 to 1,132, under the optimistic scenario of a reproduction number between 0.5 to 1. Resources and false negatives increase with the prevalence. CONCLUSIONS: the analysed screening procedure should be avoided unless the prevalence and the rate of contagion are very low. The cost and effectiveness of the screening strategies should be evaluated in the actual context of the epidemic, accounting for the fact that it may change over time.

Case-Control Study on the Routes of Transmission of SARS-CoV-2 after the Third Pandemic Wave in Tuscany, Central Italy.

The emergence of hyper-transmissible SARS-CoV-2 variants that rapidly became prevalent throughout the world in 2022 made it clear that extensive vaccination campaigns cannot represent the sole measure to stop COVID-19. However, the effectiveness of control and mitigation strategies, such as the closure of non-essential businesses and services, is debated. To assess the individual behaviours mostly associated with SARS-CoV-2 infection, a questionnaire-based case-control study was carried out in Tuscany, Central Italy, from May to October 2021. At the testing sites, individuals were invited to answer an online questionnaire after being notified regarding the test result. The questionnaire collected information about test result, general characteristics of the respondents, and behaviours and places attended in the week prior to the test/symptoms onset. We analysed 440 questionnaires. Behavioural differences between positive and negative subjects were assessed through logistic regression models, adjusting for a fixed set of confounders. A ridge regression model was also specified. Attending nightclubs, open-air bars or restaurants and crowded clubs, outdoor sporting events, crowded public transportation, and working in healthcare were associated with an increased infection risk. A negative association with infection, besides face mask use, was observed for attending open-air shows and sporting events in indoor spaces, visiting and hosting friends, attending courses in indoor spaces, performing sport activities (both indoor and outdoor), attending private parties, religious ceremonies, libraries, and indoor restaurants. These results might suggest that during the study period people maintained a particularly responsible and prudent approach when engaging in everyday activities to avoid spreading the virus.

Combining and comparing regional SARS-CoV-2 epidemic dynamics in Italy: Bayesian meta-analysis of compartmental models and global sensitivity analysis

During autumn 2020, Italy faced a second important SARS-CoV-2 epidemic wave. We explored the time pattern of the instantaneous reproductive number, R0(t), and estimated the prevalence of infections by region from August to December calibrating SIRD models on COVID-19-related deaths, fixing at values from literature Infection Fatality Rate (IFR) and average infection duration. A Global Sensitivity Analysis (GSA) was performed on the regional SIRD models. Then, we used Bayesian meta-analysis and meta-regression to combine and compare the regional results and investigate their heterogeneity. The meta-analytic R0(t) curves were similar in the Northern and Central regions, while a less peaked curve was estimated for the South. The maximum R0(t) ranged from 2.15 (South) to 2.61 (North) with an increase following school reopening and a decline at the end of October. The predictive performance of the regional models, assessed through cross validation, was good, with a Mean Absolute Percentage Error of 7.2% and 10.9% when considering prediction horizons of 7 and 14 days, respectively. Average temperature, urbanization, characteristics of family medicine and healthcare system, economic dynamism, and use of public transport could partly explain the regional heterogeneity. The GSA indicated the robustness of the regional R0(t) curves to different assumptions on IFR. The infectious period turned out to have a key role in determining the model results, but without compromising between-region comparisons.

Remote Working and Home Learning: How the Italian Academic Population Dealt with Changes Due to the COVID-19 Pandemic Lockdown

The COVID-19 pandemic introduced changes in people's lives that affected their mental health. Our study aimed to explore the level of psychological distress in the academic population during the lockdown period and investigate its association with the new working or studying conditions. The study sample included 9364 students and 2159 employees from five Italian universities from the study IO CONTO 2020. We applied linear regression models to investigate the association between home learning or remote working conditions and psychological distress, separately for students and employees. Psychological distress was assessed using the Hospital Anxiety and Depression Scale (HADS). In both students and employees, higher levels of distress were significantly associated with study/work–family conflicts, concerns about their future careers, and inadequacy of equipment;in employees, higher levels of distress were significantly associated with a lack of clarity on work objectives. Our results are in line with previous research on the impact of spaces and equipment in remote working/studying from home. Moreover, the study contributes to deepening the association between well-being and telework–family conflict, which in the literature is still equivocal. Practical implications require academic governance to promote sustainable environments both in remote and hybrid work conditions, by referring to a specific management by objectives approach.

Assessment of the feasibility of pool testing for SARS-CoV-2 infection screening.

BACKGROUND: SARS-CoV-2 pandemic represented a huge challenge for national health systems worldwide. Pooling nasopharyngeal (NP) swabs seems to be a promising strategy, saving time and resources, but it could reduce the sensitivity of the RT-PCR and exacerbate samples management in terms of automation and tracing. In this study, taking advantage of the routine implementation of a screening plan on health workers, we evaluated the feasibility of pool testing for SARS-CoV-2 infection diagnosis in the presence of low viral load samples. METHOD: Pools were prepared with an automated instrument, mixing 4, 6 or 20 NP specimens, including one, two or none positive samples. Ct values of positive samples were on average about 35 for the four genes analyzed. RESULTS: The overall sensitivity of 4-samples and 6-samples pools was 93.1 and 90.0%, respectively. Focussing on pools including one sample with Ct value ≥35 for all analyzed genes, sensitivity decreased to 77.8 and 75.0% for 4- and 6-samples, respectively; pools including two positive samples, resulted positive in any size as well as pools including positive samples with Ct values <35. CONCLUSION: Pool testing strategy should account the balance between cost-effectiveness, dilution effect and prevalence of the infection. Our study demonstrated the good performances in terms of sensitivity and saving resources of pool testing mixing 4 or 6 samples, even including low viral load specimens, in a real screening context possibly affected by prevalence fluctuation. In conclusion, pool testing strategy represents an efficient and resources saving surveillance and tracing tool, especially in specific context like schools, even for monitoring changes in prevalence associated to vaccination campaign.

Screening plans for SARS-CoV-2 based on sampling and rotation: An example in a European school setting.

Screening plans for prevention and containment of SARS-CoV-2 infection should take into account the epidemic context, the fact that undetected infected individuals may transmit the disease and that the infection spreads through outbreaks, creating clusters in the population. In this paper, we compare through simulations the performance of six screening plans based on poorly sensitive individual tests, in detecting infection outbreaks at the level of single classes in a typical European school context. The performance evaluation is done by simulating different epidemic dynamics within the class during the four weeks following the day of the initial infection. The plans have different costs in terms of number of individual tests required for the screening and are based on recurrent evaluations on all students or subgroups of students in rotation. Especially in scenarios where the rate of contagion is high, at an equal cost, testing half of the class in rotation every week appears to be better in terms of sensitivity than testing all students every two weeks. Similarly, testing one-fourth of the students every week is comparable with testing all students every two weeks, despite the first one is a much cheaper strategy. In conclusion, we show that in the presence of natural clusters in the population, testing subgroups of individuals belonging to the same cluster in rotation may have a better performance than testing all the individuals less frequently. The proposed simulations approach can be extended to evaluate more complex screening plans than those presented in the paper.

The first wave of the SARS-CoV-2 epidemic in Tuscany (Italy): A SI2R2D compartmental model with uncertainty evaluation.

With the aim of studying the spread of the SARS-CoV-2 infection in the Tuscany region of Italy during the first epidemic wave (February-June 2020), we define a compartmental model that accounts for both detected and undetected infections and assumes that only notified cases can die. We estimate the infection fatality rate, the case fatality rate, and the basic reproduction number, modeled as a time-varying function, by calibrating on the cumulative daily number of observed deaths and notified infected, after fixing to plausible values the other model parameters to assure identifiability. The confidence intervals are estimated by a parametric bootstrap procedure and a Global Sensitivity Analysis is performed to assess the sensitivity of the estimates to changes in the values of the fixed parameters. According to our results, the basic reproduction number drops from an initial value of 6.055 to 0 at the end of the national lockdown, then it grows again, but remaining under 1. At the beginning of the epidemic, the case and the infection fatality rates are estimated to be 13.1% and 2.3%, respectively. Among the parameters considered as fixed, the average time from infection to recovery for the not notified infected appears to be the most impacting one on the model estimates. The probability for an infected to be notified has a relevant impact on the infection fatality rate and on the shape of the epidemic curve. This stresses the need of collecting information on these parameters to better understand the phenomenon and get reliable predictions.

Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples.

Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the first emergency phase of the epidemic, RT-qPCR on nasopharyngeal (NP) swabs, which is the most reliable technique to detect ongoing infections, exhibited limitations due to availability of reagents and budget constraints. This stressed the need to develop screening procedures that require fewer resources and are suitable to be extended to larger portions of the population. RT-qPCR on pooled samples from individual NP swabs seems to be a promising technique to improve surveillance. We performed preliminary experimental analyses aimed to investigate the performance of pool testing on samples with low viral load and we evaluated through Monte Carlo (MC) simulations alternative screening protocols based on sample pooling, tailored to contexts characterized by different infection prevalence. We focused on the role of pool size and the opportunity to develop strategies that take advantage of natural clustering structures in the population, e.g. families, school classes, hospital rooms. Despite the use of a limited number of specimens, our results suggest that, while high viral load samples seem to be detectable even in a pool with 29 negative samples, positive specimens with low viral load may be masked by the negative samples, unless smaller pools are used. The results of MC simulations confirm that pool testing is useful in contexts where the infection prevalence is low. The gain of pool testing in saving resources can be very high, and can be optimized by selecting appropriate group sizes. Exploiting natural groups makes the definition of larger pools convenient and potentially overcomes the issue of low viral load samples by increasing the probability of identifying more than one positive in the same pool.

Psychological distress in the academic population and its association with socio-demographic and lifestyle characteristics during COVID-19 pandemic lockdown: Results from a large multicenter Italian study.

Measures implemented in many countries to contain the COVID-19 pandemic resulted in a change in lifestyle with unpredictable consequences on physical and mental health. We aimed at identifying the variables associated with psychological distress during the lockdown between April and May 2020 in the Italian academic population. We conducted a multicenter cross-sectional online survey (IO CONTO 2020) within five Italian universities. Among about 240,000 individuals invited to participate through institutional communications, 18 120 filled the questionnaire. Psychological distress was measured by the self-administered Hospital Anxiety and Depression Scale (HADS). The covariates collected included demographic and lifestyle characteristics, trust in government, doctors and scientists. Associations of covariates with influenza-like symptoms or positive COVID-19 test and with psychological distress were assessed by multiple regression models at the local level; a meta-analysis of the results was then performed. Severe levels of anxiety or depression were reported by 20% of the sample and were associated with being a student or having a lower income, irrespective of their health condition and worries about contracting the virus. The probability of being severely anxious or depressed also depended on physical activity: compared to those never exercising, the highest OR being for those who stopped during lockdown (1.53; 95% CI, 1.28 to 1.84) and the lowest for those who continued (0.78; 95% CI, 0.64 to 0.95). Up to 21% of severe cases of anxiety or depression might have been avoided if during lockdown participants had continued to exercise as before. Socioeconomic insecurity contributes to increase mental problems related to the COVID-19 pandemic and to the measures to contain it. Maintaining or introducing an adequate level of physical activity is likely to mitigate such detrimental effects. Promoting safe practice of physical activity should remain a public health priority to reduce health risks during the pandemic.

[Analysis and future scenarios of the SARS-CoV-2 epidemic in Tuscany Region (Central Italy)]. / Analisi e previsioni dell'epidemia da SARS-CoV-2 in Toscana.

OBJECTIVES: about two months after the end of the lockdown imposed for the containment of the SARS-CoV-2 epidemic, the contagion dynamics in the Tuscany Region (Central Italy) have been assessed from the beginning of the emergency to the end of June through a compartmental model, and future medium-long term projections have been produced. DATA AND METHODS: this study used a SIRD model in which the infection reproduction number R0 varied over time, according to a piecewise constant function. The fatality parameter and the time from contagion to infection resolution (death or recovery) were fixed to ensure parameter identifiability, and the model was calibrated on the Covid-19 deaths notified from March 9th to June 30th 2020. The uncertainty around the estimates was quantified through parametric bootstrap. Finally, the resulting model was used to produce medium-long term projections of the epidemic dynamics. RESULTS: the date of the first infection in Tuscany was estimated as February 21st 2020. The value of R0(t) ranged from 7.78 (95%CI 7.55-7.89), at the beginning of the outbreak, to a value very close to 0 between April 27th and May 17th. Finally, R0(t) rose, reaching an average of 0.66 (0.32, 0.88) between May 18th and June 30th. At the epidemic peak, estimated at the beginning of April, the notified infected people circulating in the region were just 22% of those predicted by the model. According to the estimated SIRD, under the hypothetical scenario that R0(t) slightly exceeds 1 from the beginning of October 2020, a new wave of contagion could arise by next spring. CONCLUSIONS: the estimated trend of R0(t) is suggestive of a strong effect of the lockdown in Tuscany and of a mild increase of the contagion potentially attributable to the easing of the containment measures. Medium-long term projections unequivocally indicate that the danger of a new epidemic wave has not been averted.