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Data and code used for the analysis in Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland (Lemaitre et al., Swiss Medial Weekly 2020).

A collection of Tweet IDs related to Covid-19 Vaccines, gathered from Twitter since Jan 4, 2021. Please see https://arxiv.org/abs/2101.07694 for more information.

By March 2020, the COVID-19 pandemic had reached Greece, forcing the Greek government to enforce lockdown for two months. While governmental measures included banning citizens' mobility, except for a six-bullets catalogue, the church was excluded, remaining open for its believers. That resulted in an official clash, having on the one side, the state and the scientists, while on the other was the official church. After the decline in the number of COVID-19 cases during the summer period, the governmental decision of enforcing the use of masks indoors triggered the rise of anti-systemic and anti-governmental rhetoric. Having the above in mind, we aim to apply a grounded theory methodology, drawing our data from two derivations: the official announcements of the church and the Greek government during the examined period; and the scientific approach to the Church's and anti-mask supporters stand. Consequently, our main research question attempts to answer how the anti-systemic rhetoric of Greek society has been transformed during the pandemic crisis.

Objective: To evaluate the effectiveness of SARS-CoV-2 testing on shortening the duration of quarantines for COVID-19 and to identify the most effective choices of testing schedules. Design: We performed extensive simulations to evaluate the performance of quarantine strategies when one or more SARS-CoV-2 tests were administered during the quarantine. Simulations were based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available testing methods. Sensitivity analyses were performed to evaluate the impact of perturbations in model assumptions on the outcomes of optimal strategies. Results: We found that SARS-CoV-2 testing can effectively reduce the length of a quarantine without compromising safety. A single RT-PCR test performed before the end of quarantine can reduce quarantine duration to 10 days. Two tests can reduce the duration to 8 days, and three highly sensitive RT-PCR tests can justify a 6-day quarantine. More strategic testing schedules and longer quarantines are needed if tests are administered with less sensitive RT-PCR tests or antigen tests. Shorter quarantines can be utilized for applications that tolerate a residual post-quarantine transmission risk comparable to a 10-day quarantine. Conclusions: Testing could substantially reduce the length of isolation, reducing the physical and mental stress caused by lengthy quarantines. With increasing capacity and lowered costs of SARS-CoV-2 tests, test-assisted quarantines could be safer and more cost-effective than 14-day quarantines and warrant more widespread use. The dataset consists of PQTR (post-quarantine transmission risk) and observed test sensitivity for test-assisted quarantine strategies with different duration and test strategies, under the assumption of either mixed and simultaneous onset of infection. PQTR is calculated as the occurrence of failures (infecting others after released from quarantine) of at least 500K (mostly 1M) replicate simulations using the simulation model described in the manuscript. The dataset is in EXCEL format. Users can open it and search for interested quarantine strategies using the filter feature of EXCEL.

For each round, a stratified random sample of approximately 7,500 adults ages 18 to 64 is drawn from the KnowledgePanel, a probability-based, nationally representative Internet panel maintained by Ipsos. The WBNS includes an oversample of adults with household incomes under 150 percent of the federal poverty level to improve the precision of estimates for this group. Current recruitment into the KnowledgePanel is based on an address-based sampling frame that covers nearly all residential addresses in the United States. In earlier periods, recruitment was carried out by telephone based on random-digit dialing sampling techniques. Approximately 55,000 U.S. households participate in the panel, including those with and without internet access. Web-enabled devices and internet access are provided to panel members if needed, and respondents can complete the online surveys in English or Spanish. In December 2017, the Urban Institute launched the Well-Being and Basic Needs Survey (WBNS), a nationally representative, internet-based survey of non-elderly adults designed to monitor changes in individual and family well-being during a time when policymakers are considering significant changes to federal safety net programs serving low-income families. The 2020 round of the survey collects information on a broad array of topics related to health, material hardship, and the safety net, including health insurance, housing, food security, employment, family income, program participation, family financial security, disability, school enrollment, child care, COVID-19 vaccine attitudes, the impact of the COVID-19 pandemic on family employment, and immigration issues. The WBNS weights reflect the probability of sample selection from the KnowledgePanel and post-stratification to the characteristics of nonelderly adults in the United States based on benchmarks from the Current Population Survey and American Community Survey for the following measures: age by gender; race and ethnicity; educational attainment; presence of children in the household; census region; residence in a metropolitan area; homeownership status; family income as a percentage of the federal poverty level; family composition (married or living with a partner by presence of children in the family); primary language; and internet access by age. web-based surveyUsers seeking the Noncitizen-Oversample (DS2) and Immigrant Module (DS3) datasets must enter a restricted data agreement with ICPSR to gain access to those datasets.This collection is related to the Well-Being and Basic Needs Survey, 2017 (ICPSR 37513), the Well-Being and Basic Needs Survey, 2018 (ICPSR 37653), and the Well-Being and Basic Needs Survey, 2019 (ICPSR 38044).Additional information about the survey is available at the Well-Being and Basic Needs Survey website. The Urban Institute launched the Well-Being and Basic Needs Survey (WBNS) to monitor changes in individual and family health and well-being as policymakers make changes to federal safety net programs and the labor market continues to evolve. Datasets: DS0: Study-Level Files DS1: Public-Use Data DS2: Noncitizen-Oversample Restricted-Use Data DS3: Immigrant Module Restricted-Use Data Response Rates: The WBNS response rate is roughly three to four percent each round. Household population aged 18-64. Smallest Geographic Unit: Census region

The emergence of newer variants with the immune escape potential raises concerns about breakthroughs and re-infections resulting in future waves of infection. We examined the protective effect of prior COVID-19 disease and vaccination on infection rates among a cohort of healthcare workers (HCW) in South India during the second wave driven mainly by the delta variant. Symptomatic HCWs were routinely tested by RT-PCR as per institutional policy. Vaccination was offered to all HCWs in late January, and the details were documented. We set up a non-concurrent cohort to document infection rates and estimated protective efficacy of prior infection and vaccination between 16th Apr to 31st May 2021, using a Cox proportional hazards model with time-varying covariates adjusting for daily incidence. Between June 2020 and May 2021, 2735 (23.9%) of 11,405 HCWs were infected, with 1412, including 32 re-infections, reported during the second wave. 6863 HCWs received two doses of vaccine and 1905 one dose. The protective efficacy of prior infection against symptomatic infection was 86.0% (95% CI 76.7% - 91.6%). Vaccination combined with prior infection provided 91.1% (95% CI 84.1% - 94.9%) efficacy. In the absence of prior infection, vaccine efficacy against symptomatic infection during the second wave was 31.8% (95% CI 23.5% – 39.1%). Prior infection provided substantial protection against symptomatic re-infection and severe disease during a delta variant-driven second wave in a cohort of health care workers. This non-concurrent cohort study was conducted among the staff of a tertiary care teaching hospital in South India. The demographic, clinical and exposure variables and vaccination history were prospectively documented in an electronic database from all those presenting for COVID testing. All immunization was documented along with the date of vaccination, type of vaccine, and any adverse events. Linking the SARS-COV2 testing data set with the vaccination and administrative payroll information, we established a non-concurrent cohort that included all current employees. Every employee has a unique employment ID which was used to match across the datasets. Two investigators independently assessed the datasets to verify the accuracy of the data and linkages between the datasets. Participants were categorized into four risk groups based on their prior infection and vaccination status, namely, the unvaccinated and previously uninfected; vaccinated and previously uninfected; unvaccinated and previously infected, and vaccinated and previously infected. A sensitivity analysis that excluded participants who had received a single dose was not significantly different from the one that included those who received one dose as unvaccinated. Hence the binary classification of vaccinated and unvaccinated was based on the completion of two doses of vaccination 2 weeks after the second dose. Kaplan Meier Survival analysis was done with failure defined as the acquisition of infection during the analysis period. A Log-rank test was performed to compare the survival curves across the four risk groups. We developed a Cox-proportional hazards (PH) model with time-varying covariates adjusting for smoothed daily incidence of COVID-19 and potential confounders (S1 table). The model included participant age, type of work, sex, history of prior infection, and vaccination, as epidemiologically relevant factors. The model was tested for the proportional-hazards assumption on Schoenfeld's residuals and the PH assumption was not violated (p-value - 0.134). Efficacy of prior infection and vaccines to prevent symptomatic infection in the study period were calculated as VE= 1- hazard ratio from the Cox proportional hazard model. All data analysis was performed using Stata 15.1 (Statacorp LLC, College Station, TX).

South-East Asia is a hot spot for emerging zoonotic diseases, and bats have been recognized as hosts for a large number of zoonotic viruses such as Severe Acute Respiratory Syndrome (SARS), responsible for acute respiratory syndrome outbreaks. Thus, it is important to expand our knowledge of the presence of viruses in bats which could represent a risk to humans. Coronaviruses (CoVs) have been reported in bat species from Thailand, China, Indonesia, Taiwan and the Philippines. However no such work was conducted in Cambodia or Lao PDR. Between 2010 and 2013, 1965 bats were therefore sampled at interfaces with human populations in these two countries. They were tested for the presence of coronavirus by consensus reverse transcription-PCR assay. A total of 93 samples (4.7%) from 17 genera of bats tested positive. Sequence analysis revealed the presence of potentially 37 and 56 coronavirus belonging to alpha-coronavirus (αCoV) and beta-CoV (βCoV), respectively. The βCoVs group is known to include some coronaviruses highly pathogenic to human, such as SARS-CoV and MERS-CoV. All coronavirus sequences generated from frugivorous bats (family Pteropodidae) (n=55) clustered with other bat βCoVs of lineage D, whereas one coronavirus from Pipistrellus coromandra fell in the lineage C of βCoVs which also includes the MERS-CoV. αCoVs were all detected in various genera of insectivorous bats and clustered with diverse bat αCoV sequences previously published. A closely related strain of PEDV, responsible for severe diarrhea in pigs (PEDV-CoV), was detected in 2 Myotis bats. We highlighted the presence and the high diversity of coronaviruses circulating in bats from Cambodia and Lao PDR. Three new bat genera and species were newly identified as host of coronaviruses, namely Macroglossus sp., Megaerops niphanae and Myotis horsfieldii. P1 Cambodia bats Coronavirus data_2019Aug16_1658Data associated with bats sampled in Cambodia and tested for CoronavirusesP1 Laos bats Coronavirus Data_2019Aug16_1656Data associated with bats sampled in Lao PDR and tested for Coronaviruses

Postural tachycardia syndrome (POTS) is a form of autonomic dysregulation. There is increasing evidence that the etiology may be immune-mediated in a subgroup of patients. Patients with POTS often experience an exacerbation of their symptoms associated with infections and often fear the same symptom aggravation after vaccination. With this data we conducted a study to describe the tolerability of mRNA vaccines against COVID-19 and the consequences of a COVID-19 infection on POTS symptoms in our cohort of patients with neuropathic POTS.We conducted a standardized, checklist-based interview with 23 patients and recorded the acute side effects of mRNA vaccination, acute symptoms of COVID-19 infection as well as the effects of vaccination and COVID-19 infection on POTS symptoms. The following side effects were assessed in their presence (yes/no) and duration (days): fever, shivering, fatigue, headache, joint pain, muscle pain, nausea, emesis, diarrhea, and reaction at injection site (pain, swelling and cutaneous reaction). For COVID-19 infection, the following additional symptoms were queried: coughing, sore throat, rhinorrhea, breathlessness, loss of taste, loss of smell and chest pain. For each symptom, the presence (yes/no), severity (mild, moderate, severe) and duration (in days) were evaluated. Furthermore, the duration of the infection, need for hospitalization and incapacity for work were assessed. To assess possible exacerbation of POTS symptoms, the presence (yes/no), severity (mild, moderate, severe; for COVID-19 infection only) and duration of symptom exacerbation (in days) for the following symptoms were evaluated: dizziness, nausea, weakness, palpitations, lightheadedness, tremulousness, blurred vision, concentration difficulties, memory difficulties, orthostatic leg and/or arm pain, gastrointestinal symptoms, sleep disturbances, restless legs syndrome and orthostatic headache. Our observations suggest that mRNA vaccines are not associated with a higher frequency of acute side effects in patients with POTS. Symptom exacerbation as a consequence of mRNA vaccination seems to be less frequent and of shorter duration compared to patients who suffered a COVID-19 infection. This study was carried out in accordance with the recommendations of the local ethics committee (Kantonale Ethikkommission Bern, Switzerland, project-ID: 2021-02115; 02.11.2021). We conducted a standardized checklist-based interview. Data analysis was descriptive.