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Hospital-based transmission had a dominant role in Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) epidemics 1,2 , but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital-community interactions. Using data from acute hospitals in England, we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 inpatients acquired SARS-CoV-2 in hospitals (1% to 2% of all hospital admissions in this period). Analysis of time series data provided evidence that patients who themselves acquired SARS-CoV-2 infection in hospital were the main sources of transmission to other patients. Increased transmission to inpatients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognized scale of hospital transmission, have direct implications for targeting of hospital control measures and highlight the need to design hospitals better equipped to limit the transmission of future high-consequence pathogens., (© 2023. The Author(s).)

Streptococcus agalactiae (group B Streptococcus) sequence type 283 bacteremia, found almost exclusively in Southeast Asia, is associated with consuming raw freshwater fish, but some patients deny consumption. We detected fecal carriage in 5/184 (2.7%) persons in northeast Thailand. Human carriers might contribute to transmission or be the original source of this sequence type.

By 22 June 2022, 521 cases of monkeypox were notified in Germany. The median age was 38 years (IQR: 32-44); all cases were men. In Berlin, where 69% of all cases occurred, almost all were men who have sex with men. Monkeypox virus likely circulated unrecognised in Berlin before early May. Since mid-May, we observed a shift from travel-associated infections to mainly autochthonous transmission that predominantly took place in Berlin, often in association with visits to clubs and parties.

Multi-state models can capture the different patterns of disease evolution. In particular, the illness-death model is used to follow disease progression from a healthy state to an intermediate state of the disease and to a death-related final state. We aim to use those models in order to adapt treatment decisions according to the evolution of the disease. In state-of-the art methods, the risks of transition between the states are modeled via (semi-) Markov processes and transition-specific Cox proportional hazard (P.H.) models. The Cox P.H. model assumes that each variable makes a linear contribution to the model, but the relationship between covariates and risks can be more complex in clinical situations. To address this challenge, we propose a neural network architecture called illness-death network (IDNetwork) that relaxes the linear Cox P.H. assumption within an illness-death process. IDNetwork employs a multi-task architecture and uses a set of fully connected subnetworks in order to learn the probabilities of transition. Through simulations, we explore different configurations of the architecture and demonstrate the added value of our model. IDNetwork significantly improves the predictive performance compared to state-of-the-art methods on a simulated data set, on two clinical trials for patients with colon cancer and on a real-world data set in breast cancer., (© 2022 John Wiley & Sons Ltd.)

Background: Health care workers (HCWs) are particularly exposed to COVID-19 and therefore it is important to study preventive measures in this population., Aim: To investigate socio-demographic factors and professional practice associated with the risk of COVID-19 among HCWs in health establishments in Normandy, France., Methods: A cross-sectional and 3 case-control studies using bootstrap methods were conducted in order to explore the possible risk factors that lead to SARS-CoV2 transmission within HCWs. Case-control studies focused on risk factors associated with (a) care of COVID-19 patients, (b) care of non COVID-19 patients and (c) contacts between colleagues., Participants: 2,058 respondents, respectively 1,363 (66.2%) and 695 (33.8%) in medical and medico-social establishments, including HCW with and without contact with patients., Results: 301 participants (14.6%) reported having been infected by SARS-CoV2. When caring for COVID-19 patients, HCWs who declared wearing respirators, either for all patient care (ORa 0.39; 95% CI: 0.29-0.51) or only when exposed to aerosol-generating procedures (ORa 0.56; 95% CI: 0.43-0.70), had a lower risk of infection compared with HCWs who declared wearing mainly surgical masks. During care of non COVID-19 patients, wearing mainly a respirator was associated with a higher risk of infection (ORa 1.84; 95% CI: 1.06-3.37). An increased risk was also found for HCWs who changed uniform in workplace changing rooms (ORa 1.93; 95% CI: 1.63-2.29)., Conclusion: Correct use of PPE adapted to the situation and risk level is essential in protecting HCWs against infection., Competing Interests: The authors have declared that no competing interests exist.

Computational fluid dynamics (CFD) modelling and 3D simulations of the air flow and dispersion of droplets or drops in semi-confined ventilated spaces have found topical applications with the unfortunate development of the Covid-19 pandemic. As an illustration of this scenario, we have considered the specific situation of a railroad coach containing a seated passenger infected with the SARS-CoV-2 virus (and not wearing a face mask) who, by breathing and coughing, releases droplets and drops that contain the virus and that present aerodynamic diameters between 1 and 1000 µm. The air flow is generated by the ventilation in the rail coach. While essentially 3D, the flow is directed from the bottom to the top of the carriage and comprises large to small eddies visualised by means of streamlines. The space and time distribution of the droplets and drops is computed using both an Eulerian model and a Lagrangian model. The results of the two modelling approaches are fully consistent and clearly illustrate the different behaviours of the drops, which fall down close to the infected passenger, and the droplets, which are carried along with the air flow and invade a large portion of the rail coach. This outcome is physically sound and demonstrates the relevance of CFD for simulating the transport and dispersion of droplets and drops with any diameter in enclosed ventilated spaces. As coughing produces drops and breathing produces droplets, both modes of transmission of the SARS-CoV-2 virus in human secretions have been accounted for in our 3D numerical study. Beyond the specific, practical application of the rail coach, this study offers a much broader scope by demonstrating the feasibility and usefulness of 3D numerical simulations based on CFD. As a matter of fact, the same computational approach that has been implemented in our study can be applied to a huge variety of ventilated indoor environments such as restaurants, performance halls, classrooms and open-plan offices in order to evaluate if their occupation could be critical with respect to the transmission of the SARS-CoV-2 virus or to other airborne respiratory infectious agents, thereby enabling relevant recommendations to be made., (© 2022. The Author(s).)

Little is known about whether and how variation in the HIV-1 genome affects its transmissibility. Assessing which genomic features of HIV-1 are under positive or negative selection during transmission is challenging, because very few virus particles are typically transmitted, and random genetic drift can dilute genetic signals in the recipient virus population. We analyzed 30 transmitter-recipient pairs from the Zurich Primary HIV Infection Study and the Swiss HIV Cohort Study using near full-length HIV-1 genomes. We developed a new statistical test to detect selection during transmission, called Selection Test in Transmission (SeTesT), based on comparing the transmitter and recipient virus population and accounting for the transmission bottleneck. We performed extensive simulations and found that sensitivity of detecting selection during transmission is limited by the strong population bottleneck of few transmitted virions. When pooling individual test results across patients, we found two candidate HIV-1 genomic features for affecting transmission, namely amino acid positions 3 and 18 of Vpu, which were significant before but not after correction for multiple testing. In summary, SeTesT provides a general framework for detecting selection based on genomic sequencing data of transmitted viruses. Our study shows that a higher number of transmitter-recipient pairs is required to improve sensitivity of detecting selection.

The coronavirus disease 2019 (COVID-19) pandemic became an important public health problem affecting all age groups. The aim of this study was to evaluate clinical and laboratory findings of newborns born to mothers with COVID-19. Thirty pregnant women with COVID-19 were admitted to Turgut Ozal University Hospital for delivery. Fourteen pregnant women had at least one symptom associated with COVID-19. Positive polymerase chain reaction (PCR) results were seen in only 3 (9.7%) of 31 newborns. A statistically significant difference was observed between PCR-positive and PCR-negative newborns in terms of any adverse pregnancy outcomes. Neonatal lymphocyte count and partial arterial oxygen pressure were significantly lower in the PCR-positive group. Results were also compared according to the interval from the maternal diagnosis time to delivery. Hemoglobin and hematocrit levels in newborns born to mothers diagnosed more than 7 days before delivery were significantly lower. Neonates born to mothers with COVID-19 had mild clinical symptoms and favorable outcomes.

The transmission of COVID-19 is dependent on social mixing, the basic rate of which varies with sociodemographic, cultural, and geographic factors. Alterations in social mixing and subsequent changes in transmission dynamics eventually affect hospital admissions. We employ these observations to model and predict regional hospital admissions in Sweden during the COVID-19 pandemic. We use an SEIR-model for each region in Sweden in which the social mixing is assumed to depend on mobility data from public transport utilisation and locations for mobile phone usage. The results show that the model could capture the timing of the first and beginning of the second wave of the pandemic 3 weeks in advance without any additional assumptions about seasonality. Further, we show that for two major regions of Sweden, models with public transport data outperform models using mobile phone usage. We conclude that a model based on routinely collected mobility data makes it possible to predict future hospital admissions for COVID-19 3 weeks in advance., (© 2021. The Author(s).)

Objectives: To explore the potential of SARS-CoV-2 spread during air travel and the risk of in-flight transmission., Methods: We enrolled all passengers and crew suspected of being infected with SARS-CoV-2, who bounded for Beijing on international flights. We specified the characteristics of all confirmed cases of COVID-19 infection and utilised Wells-Riley equation to estimate the infectivity of COVID-19 during air travel., Results: We screened 4492 passengers and crew with suspected COVID-19 infection, verified 161 confirmed cases (mean age 28.6 years), and traced two confirmed cases who may have been infected in the aircraft. The estimated infectivity was 375 quanta/h (range 274-476), while the effective infectivity was only 4 quanta/h (range 2-5). The risk of per-person infection during a 13 h air travel in economy class was 0.56‰ (95% CI 0.41‰-0.72‰)., Conclusion: We found that the universal use of face masks on the flight, together with the plane's ventilation system, significantly decreased the infectivity of COVID-19.KEY MESSAGESThe COVID-19 pandemic is changing the lifestyle in the world, especially air travel which has the potential to spread SARS-CoV-2.The universal use of face masks on the flight, together with the plane's ventilation system, significantly decreased the infectivity of COVID-19 on an aircraft.Our findings suggest that the risk of infection in aircraft was negligible.

The COVID-19 pandemic has been particularly threatening to patients with end-stage kidney disease (ESKD) on intermittent hemodialysis and their care providers. Hemodialysis patients who receive life-sustaining medical therapy in healthcare settings, face unique challenges as they need to be at a dialysis unit three or more times a week, where they are confined to specific settings and tended to by dialysis nurses and staff with physical interaction and in close proximity. Despite the importance and critical situation of the dialysis units, modelling studies of the SARS-CoV-2 spread in these settings are very limited. In this paper, we have used a combination of discrete event and agent-based simulation models, to study the operations of a typical large dialysis unit and generate contact matrices to examine outbreak scenarios. We present the details of the contact matrix generation process and demonstrate how the simulation calculates a micro-scale contact matrix comprising the number and duration of contacts at a micro-scale time step. We have used the contacts matrix in an agent-based model to predict disease transmission under different scenarios. The results show that micro-simulation can be used to estimate contact matrices, which can be used effectively for disease modelling in dialysis and similar settings., Competing Interests: The authors have declared that no competing interests exist.

The SARS-CoV-2 virus is highly contagious, as demonstrated by numerous well-documented superspreading events. The infection commonly starts in the upper respiratory tract (URT) but can migrate to the lower respiratory tract (LRT) and other organs, often with severe consequences. Whereas LRT infection can lead to shedding of virus via breath and cough droplets, URT infection enables shedding via abundant speech droplets. Their viral load can be high in carriers with mild or no symptoms, an observation linked to the abundance of SARS-CoV-2-susceptible cells in the oral cavity epithelium. Expelled droplets rapidly lose water through evaporation, with the smaller ones transforming into long-lived aerosol. Although the largest speech droplets can carry more virions, they are few in number, fall to the ground rapidly and therefore play a relatively minor role in transmission. Of more concern is small speech aerosol, which can descend deep into the LRT and cause severe disease. However, since their total volume is small, the amount of virus they carry is low. Nevertheless, in closed environments with inadequate ventilation, they can accumulate, which elevates the risk of direct LRT infection. Of most concern is the large fraction of speech aerosol that is intermediate-sized because it remains suspended in air for minutes and can be transported over considerable distances by convective air currents. The abundance of this speech-generated aerosol, combined with its high viral load in pre- and asymptomatic individuals, strongly implicates airborne transmission of SARS-CoV-2 through speech as the primary contributor to its rapid spread., (© 2021 Association for Publication of The Journal of Internal Medicine.)

Objectives/hypothesis: Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is transmitted by droplet as well as airborne infection. Surgical patients are vulnerable to the infection during their hospital admission. Some surgical procedures are classified as aerosol generating (AGP)., Study Design: Retrospective observational study of four specialties associates with known AGP's during the 4 months of the first wave of UK COVID-19 epidermic to identify post-surgical cross-infection with SARSCoV-2 within 14 days of a procedure., Methods: Retrospective observational study in a tertiary healthcare center of four specialties associates with known AGP's during the 4 months of the first wave of UK COVID-19 epidermic to identify post-surgical cross-infection with SARSCoV-2 within 14 days of a procedure., Results: There were 3,410 procedures reported during this period. The overall cross-infection rate from tested patients was 1.3% (4 patients), that is, 0.11% of all operations over 4 months. Ear, nose, and throat carried slightly higher rate of infection (0.4%) than gastroenterology (0.08%). The mortality rate was 0.3% (one gastroenterology patient from 304 positive cases) compared to 0% if surgery performed after recovery from SARSCoV-2 and 37.5% when surgery was conducted during the incubation period of the disease. Routine preoperative rapid screening tests and self-isolation are crucial to avoid the risk of cross-infection. Patients with underlying malignancy or receiving chemotherapy were more prone to pulmonary complications and mortality., Conclusion: The risk of SARS-COV-2 cross-infection after surgical procedure is very low. Preoperative screening and self-isolation together with personal protective measures should be in place to minimize the cross-infection., Level of Evidence: 4 Laryngoscope, 131:E2749-E2754, 2021., (© 2021 The American Laryngological, Rhinological and Otological Society, Inc.)

Competing Interests: The authors report no conflicts of interest.

In this study, two types of epidemiological models called "within host" and "between hosts" have been studied. The within-host model represents the innate immune response, and the between-hosts model signifies the SEIR (susceptible, exposed, infected, and recovered) epidemic model. The major contribution of this paper is to break the chain of infectious disease transmission by reducing the number of susceptible and infected people via transferring them to the recovered people group with vaccination and antiviral treatment, respectively. Both transfers are considered with time delay. In the first step, optimal control theory is applied to calculate the optimal final time to control the disease within a host's body with a cost function. To this end, the vaccination that represents the effort that converts healthy cells into resistant-to-infection cells in the susceptible individual's body is used as the first control input to vaccinate the susceptible individual against the disease. Moreover, the next control input (antiviral treatment) is applied to eradicate the concentrations of the virus and convert healthy cells into resistant-to-infection cells simultaneously in the infected person's body to treat the infected individual. The calculated optimal time in the first step is considered as the delay of vaccination and antiviral treatment in the SEIR dynamic model. Using Pontryagin's maximum principle in the second step, an optimal control strategy is also applied to an SEIR mathematical model with a nonlinear transmission rate and time delay, which is computed as optimal time in the first step. Numerical results are consistent with the analytical ones and corroborate our theoretical results., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2021 Zohreh Abbasi et al.)

Background: Israel has experienced three waves of coronavirus disease-2019 (COVID-19) infection since late February 2020, with lockdown and other measures employed to contain infection rates. In cooperation with the Israel Ministry of Health, serological testing was conducted by all four health maintenance organizations (HMO) in order to estimate national infection rates and the proportion of previously undetected disease., Objectives: To estimate the proportion of the population that was seropositive, identify factors associated with seropositive outcome, and approximate the proportion of residents that were asymptomatic., Methods: Seroconversion rates (IgG) were measured in a representative sample of over 17,000 members of Maccabi Healthcare Services. Direct standardization was used to estimate the seropositive rates for COVID-19 infection for members of the HMO. Rates were adjusted for sensitivity and specificity of the testing products used. In addition to blood sampling, respondents were asked to complete a digital survey regarding potential exposures and symptoms experienced., Results: It was estimated that 1.9% of the adult HMO population was seropositive 4 months after the first infected person was identified in the country. Seroconversion was associated with travel abroad and exposure to infected individuals. Loss of smell and taste, fever, cough, and fatigue are associated with infection. Of those found to be seropositive for COVID-19, 160 (59%) had a prior negative polymerase chain reaction (PCR) or no PCR test at all., Conclusions: Adult seropositive rates of infection were low relative to other countries. The findings suggest that early initiatives to limit infection entry and spread were effective.

The complexities involved in modelling the transmission dynamics of COVID-19 has been a roadblock in achieving predictability in the spread and containment of the disease. In addition to understanding the modes of transmission, the effectiveness of the mitigation methods also needs to be built into any effective model for making such predictions. We show that such complexities can be circumvented by appealing to scaling principles which lead to the emergence of universality in the transmission dynamics of the disease. The ensuing data collapse renders the transmission dynamics largely independent of geopolitical variations, the effectiveness of various mitigation strategies, population demographics, etc. We propose a simple two-parameter model-the Blue Sky model-and show that one class of transmission dynamics can be explained by a solution that lives at the edge of a blue sky bifurcation. In addition, the data collapse leads to an enhanced degree of predictability in the disease spread for several geographical scales which can also be realized in a model-independent manner as we show using a deep neural network. The methodology adopted in this work can potentially be applied to the transmission of other infectious diseases and new universality classes may be found. The predictability in transmission dynamics and the simplicity of our methodology can help in building policies for exit strategies and mitigation methods during a pandemic., (© 2021. The Author(s).)

Importance: Staphylococcus aureus is one of the leading causes of infections in neonatal intensive care units (NICUs). Most studies in this patient group focus on methicillin-resistant S aureus or the outbreak setting, whereas data for methicillin-susceptible S aureus are limited., Objectives: To identify risk factors for S aureus colonization and infections in hospitalized newborns and to investigate S aureus transmission and its dynamics in a nonoutbreak setting., Design, Setting, and Participants: This monocentric cohort study in a tertiary NICU in Heidelberg, Germany, enrolled all hospitalized neonates (n = 590) with at least 1 nasal screening swab positive for S aureus. Data were collected from January 1, 2018, to December 31, 2019., Exposures: Weekly screening for S aureus colonization was performed for all newborns until discharge., Main Outcomes and Measures: The primary end point was any S aureus infection until hospital discharge. Transmission of S aureus and performance of routine typing to detect transmissions were defined as the secondary outcomes of the study., Results: In total, 590 newborns were enrolled (276 [46.8%] female and 314 [53.2%] male; 220 [37.3%] with birthweight <1500 g; 477 [80.8%] preterm; 449 [76.1%] singletons; 419 [71.5%] delivered via cesarean section). The median length of stay was 26 (range, 10-62) days. Overall, 135 infants (22.9%) were colonized by S aureus at some time during their hospital stay. The median time to first detection was 17 (interquartile range, 11-37) days. The overall incidence of S aureus infection was 1.7% (10 of 590). Low birth weight (<1500 g [odds ratio, 9.3; 95% CI, 5.9-14.6; P < .001]) and longer hospital stay (odds ratio, 2.3; 95% CI, 1.9-2.7; P < .001) were associated with colonization. Nasal carriage was significantly associated with S aureus infection (odds ratio, 8.2; 95% CI, 2.1-32.3; P = .002). A total of 123 of 135 colonization isolates were sequenced. All recoverable infection isolates (4 of 7) of newborns with colonization were genetically identical to the colonizing isolate. Whole-genome sequencing indicated 23 potential transmission clusters., Conclusions and Relevance: The findings of this cohort study suggest that nasal colonization is a relevant risk factor for S aureus infection in a nonoutbreak NICU setting. In colonized newborns, infection and colonization isolates were genetically identical, suggesting that eradication of colonization may be a useful measure to prevent infection. Further investigations are necessary to validate and assess the generalizability of our findings.

Since December 2019, the novel COVID-19 outbreak has spread rapidly around the globe and infected millions of people. Although the major transmission route of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered to be airborne droplets and close contact, the ocular transmission route has been reported with great concern. The current work summarises the characteristics of SARS-CoV-2, the ocular distribution of the major SARS-CoV-2 binding protein, and the experimental and clinical evidence of the ocular transmission route. Although it seems that the likelihood of the ocular surface being an infection gateway is low, SARS-CoV-2 infection or transmission via the ocular surface may cause conjunctivitis and other ocular discomfort. Therefore, good eye protection is an essential safeguard procedure, especially for medical staff., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

CRF19 is a recombinant form of HIV-1 subtypes D, A1 and G, which was first sampled in Cuba in 1999, but was already present there in 1980s. CRF19 was reported almost uniquely in Cuba, where it accounts for ∼25% of new HIV-positive patients and causes rapid progression to AIDS (∼3 years). We analyzed a large data set comprising ∼350 pol and env sequences sampled in Cuba over the last 15 years and ∼350 from Los Alamos database. This data set contained both CRF19 (∼315), and A1, D and G sequences. We performed and combined analyses for the three A1, G and D regions, using fast maximum likelihood approaches, including: (1) phylogeny reconstruction, (2) spatio-temporal analysis of the virus spread, and ancestral character reconstruction for (3) transmission mode and (4) drug resistance mutations (DRMs). We verified these results with a Bayesian approach. This allowed us to acquire new insights on the CRF19 origin and transmission patterns. We showed that CRF19 recombined between 1966 and 1977, most likely in Cuban community stationed in Congo region. We further investigated CRF19 spread on the Cuban province level, and discovered that the epidemic started in 1970s, most probably in Villa Clara, that it was at first carried by heterosexual transmissions, and then quickly spread in the 1980s within the "men having sex with men" (MSM) community, with multiple transmissions back to heterosexuals. The analysis of the transmission patterns of common DRMs found very few resistance transmission clusters. Our results show a very early introduction of CRF19 in Cuba, which could explain its local epidemiological success. Ignited by a major founder event, the epidemic then followed a similar pattern as other subtypes and CRFs in Cuba. The reason for the short time to AIDS remains to be understood and requires specific surveillance, in Cuba and elsewhere., Competing Interests: The authors have declared that no competing interests exist.

Wearing a facial mask can limit COVID-19 transmission. Measurements of communities' mask use behavior have mostly relied on self-report. This study's objective was to devise a method to measure the prevalence of improper mask use and no mask use in indoor public areas without relying on self-report. A stratified random sample of retail trade stores (public areas) in Louisville, Kentucky, USA, was selected and targeted for observation by trained surveyors during December 14-20, 2020. The stratification allowed for investigating mask use behavior by city district, retail trade group, and public area size. The total number of visited public areas was 382 where mask use behavior of 2,080 visitors and 1,510 staff were observed. The average prevalence of mask use among observed visitors was 96%, while the average prevalence of proper use was 86%. In 48% of the public areas, at least one improperly masked visitor was observed and in 17% at least one unmasked visitor was observed. The average prevalence of proper mask use among staff was 87%, similar to the average among visitors. However, the percentage of public areas where at least one improperly masked staff was observed was 33. Significant disparities in mask use and its proper use were observed among both visitors and staff by public area size, retail trade type, and geographical area. Observing unmasked and improperly masked visitors was more common in small (less than 1500 square feet) public areas than larger ones, specifically in food and grocery stores as compared to other retail stores. Also, the majority of the observed unmasked persons were male and middle-aged., Competing Interests: No authors have competing interests.

Background: Governments across the globe responded with different strategies to the COVID-19 pandemic. While some countries adopted measures, which have been perceived controversial, others pursued a strategy aiming for herd immunity. The latter is even more controversial and has been called unethical by the WHO Director-General. Inevitably, without proper control measures, viral diversity increases and multiple infectious exposures become common, when the pandemic reaches its maximum. This harbors not only a potential threat overseen by simplified theoretical arguments in support of herd immunity, but also deserves attention when assessing response measures to increasing numbers of infection., Methods and Findings: We extend the simulation model underlying the pandemic preparedness web interface CovidSim 1.1 (http://covidsim.eu/) to study the hypothetical effect of increased morbidity and mortality due to 'multi-infections', either acquired at by successive infective contacts during the course of one infection or by a single infective contact with a multi-infected individual. The simulations are adjusted to reflect roughly the situation in the USA. We assume a phase of general contact reduction ("lockdown") at the beginning of the epidemic and additional case-isolation measures. We study the hypothetical effects of varying enhancements in morbidity and mortality, different likelihoods of multi-infected individuals to spread multi-infections and different susceptibility to multi-infections in different disease phases. It is demonstrated that multi-infections lead to a slight reduction in the number of infections, as these are more likely to get isolated due to their higher morbidity. However, the latter substantially increases the number of deaths. Furthermore, simulations indicate that a potential second lockdown can substantially decrease the epidemic peak, the number of multi-infections and deaths., Conclusions: Enhanced morbidity and mortality due to multiple disease exposure is a potential threat in the COVID-19 pandemic that deserves more attention. Particularly it underlines another facet questioning disease management strategies aiming for herd immunity., Competing Interests: The authors have declared that no competing interests exist.

Background: In response to the spread of the coronavirus disease 2019 (COVID-19), plenty of control measures were proposed. To assess the impact of current control measures on the number of new case indices 14 countries with the highest confirmed cases, highest mortality rate, and having a close relationship with the outbreak's origin; were selected and analyzed., Methods: In the study, we analyzed the impact of five control measures, including centralized isolation of all confirmed cases, closure of schools, closure of public areas, closure of cities, and closure of borders of the 14 targeted countries according to their timing; by comparing its absolute effect average, its absolute effect cumulative, and its relative effect average., Results: Our analysis determined that early centralized isolation of all confirmed cases was represented as a core intervention in significantly disrupting the pandemic's spread. This strategy helped in successfully controlling the early stage of the outbreak when the total number of cases were under 100, without the requirement of the closure of cities and public areas, which would impose a negative impact on the society and its economy. However, when the number of cases increased with the apparition of new clusters, coordination between centralized isolation and non-pharmaceutical interventions facilitated control of the crisis efficiently., Conclusion: Early centralized isolation of all confirmed cases should be implemented at the time of the first detected infectious case., Competing Interests: The authors have declared that no competing interests exist.

In the current study, we followed 839 household contacts (HHCs) of tuberculosis (TB) patients for 2 years and identified the factors that enhanced the development of TB. Fourteen of the 17 HHCs who progressed to TB were in the 15- to 30-year-old age group. At baseline (the "0" time point, when all the individuals were healthy), the concentration of the thyroid hormone thyroxine (T4) was lower, and there were increased numbers of Tregs in PBMCs of TB progressors. At baseline, PBMCs from TB progressors stimulated with early secretory antigenic target 6 (ESAT-6) and 10 kDa culture filtrate antigen (CFP-10) produced less IL-1α. Thyroid hormones inhibited Mycobacterium tuberculosis (Mtb) growth in macrophages in an IL-1α-dependent manner. Mtb-infected Thra1PV/+ (mutant thyroid hormone receptor) mice had increased mortality and reduced IL-1α production. Our findings suggest that young HHCs who exhibit decreased production of thyroid hormones are at high risk of developing active TB disease.

Competing Interests: Competing interests: Leyla Asadi reports receiving a grant from the Alberta Health Innovates Clinician Fellowship. No other competing interests were declared.

Importance: Clinical data are lacking regarding the risk of viral transmission from individuals who have positive reverse-transcription-polymerase chain reaction (RT-PCR) SARS-CoV-2 test results after recovery from COVID-19., Objective: To describe case characteristics, including viral dynamics and transmission of infection, for individuals who have clinically recovered from SARS-CoV-2 infection but continued to have positive test results following discontinuation of isolation precautions., Design, Setting, and Participants: This retrospective cohort study used data collected from June 11, 2020, to October 19, 2020, as part of the National Basketball Association (NBA) closed campus occupational health program in Orlando, Florida, which required daily RT-PCR testing and ad hoc serological testing for SARS-CoV-2 IgG antibodies. Nearly 4000 NBA players, staff, and vendors participated in the NBA's regular and postseason occupational health program in Orlando. Persistent positive cases were those who recovered from a documented SARS-CoV-2 infection, satisfied US Centers for Disease Control and Prevention criteria for discontinuation of isolation precautions, and had at least 1 postinfection positive RT-PCR test(s) result., Exposures: Person-days of participation in indoor, unmasked activities that involved direct exposure between persistent positive cases and noninfected individuals., Main Outcomes and Measures: Transmission of SARS-CoV-2 following interaction with persistent positive individuals, as measured by the number of new COVID-19 cases in the Orlando campus program., Results: Among 3648 individuals who participated, 36 (1%) were persistent positive cases, most of whom were younger than 30 years (24 [67%]) and male (34 [94%]). Antibodies were detected in 33 individuals (91.7%); all remained asymptomatic following the index persistent positive RT-PCR result. Cycle threshold values for persistent positive RT-PCR test results were typically above the Roche cobas SARS-CoV-2 limit of detection. Cases were monitored for up to 100 days (mean [SD], 51 [23.9] days), during which there were at least 1480 person-days of direct exposure activities, with no transmission events or secondary infections of SARS-CoV-2 detected (0 new cases)., Conclusions and Relevance: In this retrospective cohort study of the 2020 NBA closed campus occupational health program, recovered individuals who continued to test positive for SARS-CoV-2 following discontinuation of isolation were not infectious to others. These findings support time-based US Centers of Disease Control and Prevention recommendations for ending isolation.

We performed large-scale numerical simulations using a composite model to investigate the infection spread in a supermarket during a pandemic. The model is composed of the social force, purchasing strategy and infection transmission models. Specifically, we quantified the infection risk for customers while in a supermarket that depended on the number of customers, the purchase strategies and the physical layout of the supermarket. The ratio of new infections compared to sales efficiency (earned profit for customer purchases) was computed as a factor of customer density and social distance. Our results indicate that the social distance between customers is the primary factor influencing infection rate. Supermarket layout and purchasing strategy do not impact social distance and hence the spread of infection. Moreover, we found only a weak dependence of sales efficiency and customer density. We believe that our study will help to establish scientifically-based safety rules that will reduce the social price of supermarket business., Competing Interests: The authors have declared that no competing interests exist.

Background: Clusters of COVID-19 cases amplify the pandemic and are critical targets for intervention, but comprehensive cluster-level data are not collected systematically by federal or most state public health entities. This analysis characterizes COVID-19 clusters among vulnerable populations housed in congregate living settings across an entire community and describes early mitigation efforts., Methods: The Cuyahoga County Board of Health identified and interviewed COVID-19 cases and exposed contacts, assessing possible connections to congregate living facilities within its jurisdiction from March 7, 2020, to May 15, 2020, during the first phase of the pandemic, while state of Ohio stay-at-home orders were in effect. A multi-disciplinary team-based response network was mobilized to support active case finding and develop facility-focused containment strategies., Results: We identified a cascade of 45 COVID-19 clusters across community facilities (corrections, nursing, assisted living, intermediate care, extended treatment, shelters, group homes). Attack rates were highest within small facilities (P < .01) and large facilities requiring extensive support to implement effective containment measures. For 25 clusters, we identified an index case who frequently (88%) was a healthcare worker. Engagement of clinical, community, and government partners through public health coordination efforts created opportunities to rapidly develop and coordinate effective response strategies to support the facilities facing the dawning impact of the pandemic., Conclusions: Active cluster investigations can uncover the dynamics of community transmission affecting both residents of congregate settings and their caregivers and help to target efforts toward populations with ongoing challenges in access to detection and control resources., (© 2020 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.)

Background: This article reports the results of a rapid scoping review of the literature on COVID-19 transmission risk to workers in essential sectors such as retail, health care, manufacturing, and agriculture, and more particularly the experiences of workers in precarious employment and social situations., Methods: Following scoping review methods, we included 30 studies that varied in terms of methodology and theoretical approaches. The search included peer-reviewed articles and grey literature published between March and September 2020., Results: Based on the studies reviewed, we found that COVID-19 infection and death rates increased not only with age and comorbidities, but also with discrimination and structural inequities based on racism and sexism. Racial and ethnic minority workers, including migrant workers, are concentrated in high-risk occupations and this concentration is correlated to lower socioeconomic conditions. The COVID-19 pandemic appears in the occupational health and safety spotlight as an exacerbator of already existing socioeconomic inequalities and social inequalities in health, especially in light of the intersection of issues related to racism, ethnic minority status, and sexism., Conclusions: This review provides early evidence about the limitations of institutions' responses to the pandemic, and their capacity to provide a safe and decent working environment for all workers, regardless of their employment status or the social protections they may enjoy under normal circumstances. It is also important to think about these issues in the postpandemic context, when conditions of precariousness and vulnerability persist and possibly worsen., (© 2021 Wiley Periodicals LLC.)

Background: Children who inhabit the same house with tuberculosis (TB) patients are at high risk for infection and illness with TB. Nutritional status (stunting) in children is related to the child's ability to withstand MTB (Mycobacterium Tuberculosis). This study aims to estimated the prevalence of tuberculosis infection and its relationship to stunting in children (under five years) with household contact (HHC) with new TB cases., Methods: A cross-sectional design was implemented. Conducted in July 2018-April 2019 at 13 Public Health Center in Makassar City. The sample size was calculated using one sample situation-about precision formula. Samples were children under five who had contact with new diagnosed TB cases. Tuberculosis infection was measured by TST (tuberculin skin test). Logistic regression with causal model to examine TB infection relationship with stunting and covariate variable, analyzed using Stata/MP 13.0 software., Results: One hundred twenty-six (126) eligible children. Prevalence of tuberculosis infection was 38.10%. Frequency of stunted was 31 children (24.60%). Stunted nutritional status (aPR): 2.36, 95% CI 1.60-3.44), boys (aPR: 1.47, 95% CI 0.96-2.25), not getting BCG immunization (aPR: 1.58, 95%) CI 0.89-2.82), and high contact intensity (aPR: 2.62, 95% CI 1.10-6.22) best predicted the tuberculosis infection in children with TB case household contacts with a model contribution of 64%., Conclusion: Stunted nutritional status (moderate and severe), boys, not getting BCG immunization, and high contact intensity are the determinants of TB infection transmission in children HHC with TB. Children under five years of age who have close contact with TB cases should be targeted for priority interventions to prevent the transmission of TB infection and progressing to TB cases., Competing Interests: Conflicts of interest The authors have none to declare., (Copyright © 2020 Tuberculosis Association of India. Published by Elsevier B.V. All rights reserved.)

Background/aim: COVID-19 syndrome due to the SARS-CoV-2 virus is a currently challenging situation ongoing worldwide. Since the current pandemic of the SARS-CoV-2 virus is a great concern for everybody in the World, the frequently asked question is how and when the COVID-19 process will be concluded. The aim of this paper is to propose hypotheses in order to answer this essential question. As recently demonstrated, SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the human genome. Our main hypothesis is that the ultimate aim of the SARS-CoV-2 virus is the incorporation to human genome and being an element of the intestinal virobiota., Materials and Methods: We propose that the SARS-CoV-2 genomic incorporation to be a part of human virobiota is essentially based on three pathobiological phases which are called as the ‘induction’, ‘consolidation’, and ‘maintenance phases’. The phase of ‘recurrence’ complicates any of these three disease phases based on the viral load, exposure time, and more contagious strains and/or mutants. We have performed the ‘random walk model’ in order to predict the community transmission kinetics of the virus., Results: Chimerism-mediated immunotherapy at the individual and community level with the help of vaccination seems to be the only option for ending the COVID-19 process. After the integration of SARS-CoV-2 virus into the human genome via the induction, consolidation, and maintenance phases as an element of intestinal virobiota, the chimerism would be concluded. The ‘viral load’, the ‘genomic strain of the SARS-CoV-2’, and ‘host immune reaction against the SARS-CoV-2’ are the hallmarks of this long journey., Conclusion: Elucidation of the functional viral dynamics will be helpful for disease management at the individual- and community- based long-term management strategies., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (This work is licensed under a Creative Commons Attribution 4.0 International License.)

Objective: To evaluate if Healthcare workers (HCWs) at the frontline of COVID-19 response in a pediatric hospital are at an increased risk of acquiring SARS-CoV-2., Methods: The Hospital Infection Control Committee (HICC) and virology testing records were combined to identify SARS-CoV-2 positive HCWs and study the transmission dynamics of COVID-19 over 6 months., Results: COVID-19 cases in our HCWs cohort rose and declined parallel to community cases. Forty two out of 534 HCWs (8%) were SARS-CoV-2 positive with no fatalities. No clinical staff in the special COVID ward or ICU was positive. Significant proportion of non-clinical staff (30%) were SARS-CoV-2 positive. About 70% of SARS-CoV-2 positive staff had likely community acquisition, with a significant proportion having travelled by public transport or having a contact history with a positive case in the community. Twenty four percent of positive staff were asymptomatic and detected positive on re-joining test., Conclusions: Sustained transmission of SARS-CoV-2 did not occur in our cohort beyond community transmission. Appropriate PPE use, strict and constantly improving infection control measures and testing of both clinical and non-clinical staff were essential methods for restricting transmission amongst HCWs.

Vaccination is the most efficient means of preventing influenza infection and its complications. While previous studies have considered the externalities of vaccination that arise from indirect protection against influenza infection, they have often neglected another key factor-the spread of vaccination behavior among social contacts. We modeled influenza vaccination as a socially contagious process. Our model uses a contact network that we developed based on aggregated and anonymized mobility data from the cellphone devices of ~1.8 million users in Israel. We calibrated the model to high-quality longitudinal data of weekly influenza vaccination uptake and influenza diagnoses over seven years. We demonstrate how a simple coupled-transmission model accurately captures the spatiotemporal patterns of both influenza vaccination uptake and influenza incidence. Taking the identified complex underlying dynamics of these two processes into account, our model determined the optimal timing of influenza vaccination programs. Our simulation shows that in regions where high vaccination coverage is anticipated, vaccination uptake would be more rapid. Thus, our model suggests that vaccination programs should be initiated later in the season, to mitigate the effect of waning immunity from the vaccine. Our simulations further show that optimally timed vaccination programs can substantially reduce disease transmission without increasing vaccination uptake., Competing Interests: The authors have declared that no competing interests exist.

Background: The ongoing SARS-CoV-2 pandemic has spread rapidly worldwide and disease prevention is more important than ever. In the absence of a vaccine, knowledge of the transmission routes and risk areas of infection remain the most important existing tools to prevent further spread., Methods: Here we investigated the presence of the SARS-CoV-2 virus in the hospital environment at the Uppsala University Hospital Infectious Disease ward by RT-qPCR and determined the infectivity of the detected virus in vitro on Vero E6 cells., Results: SARS-CoV-2 RNA was detected in several areas, although attempts to infect Vero E6 cells with positive samples were unsuccessful. However, RNase A treatment of positive samples prior to RNA extraction did not degrade viral RNA, indicating the presence of SARS-CoV-2 nucleocapsids or complete virus particles protecting the RNA as opposed to free viral RNA., Conclusion: Our results show that even in places where a moderate concentration (Ct values between 30 and 38) of SARS-CoV-2 RNA was found; no infectious virus could be detected. This suggests that the SARS-CoV-2 virus in the hospital environment subsides in two states; as infectious and as non-infectious. Future work should investigate the reasons for the non-infectivity of SARS-CoV-2 virions.

Coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2), has claimed many victims worldwide due to its high virulence and contagiousness. The person-to-person transmission of SARS-Cov-2 when in close contact is facilitated by respiratory droplets containing the virus particles, and by skin contact with contaminated surfaces. However, the large number of COVID-19 infections cannot be explained only by droplet deposition or contact contamination. It seems very plausible that aerosols are important in transmitting SARS-Cov-2. It has been demonstrated that SARS-CoV-2 remains viable in aerosols for hours, facilitating rapid distribution of the virus over great distances. Aerosols may, therefore, also be responsible for so-called super-spreader events. Indirect evidence points to a correlation between ventilation and the transmission and spread of SARS-Cov-2, supporting ventilation as an important factor in preventing airborne transmission. Further actions to avoid transmission of COVID-19 include social distancing, hygiene measures, and barrier measures, such as face-coverings. Professional masks offer better protection than cloth masks. These protection measures are especially relevant to health care workers, when performing endotracheal intubation, but the risk from non-invasive ventilation and nebulizing treatment seems to be moderate., Competing Interests: The authors report no conflict of interest., (Copyright © 2021 American College of Occupational and Environmental Medicine.)

Background: Infection fatality rate and infection hospitalization rate, defined as the proportion of deaths and hospitalizations, respectively, of the total infected individuals, can estimate the actual toll of coronavirus disease 2019 (COVID-19) on a community, as the denominator is ideally based on a representative sample of a population, which captures the full spectrum of illness, including asymptomatic and untested individuals., Objective: To determine the COVID-19 infection hospitalization rate and infection fatality rate among the non-congregate population in Connecticut between March 1 and June 1, 2020., Methods: The infection hospitalization rate and infection fatality rate were calculated for adults residing in non-congregate settings in Connecticut prior to June 2020. Individuals with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies were estimated using the seroprevalence estimates from the recently conducted Post-Infection Prevalence study. Information on total hospitalizations and deaths was obtained from the Connecticut Hospital Association and the Connecticut Department of Public Health, respectively., Results: Prior to June 1, 2020, nearly 113,515 (90% confidence interval [CI] 56,758-170,273) individuals were estimated to have SARS-CoV-2 antibodies, and there were 7792 hospitalizations and 1079 deaths among the non-congregate population. The overall COVID-19 infection hospitalization rate and infection fatality rate were estimated to be 6.86% (90% CI, 4.58%-13.72%) and 0.95% (90% CI, 0.63%-1.90%), respectively, and there was variation in these rate estimates across subgroups; older people, men, non-Hispanic Black people, and those belonging to 2 of the counties had a higher burden of adverse outcomes, although the differences between most subgroups were not statistically significant., Conclusions: Using representative seroprevalence estimates, the overall COVID-19 infection hospitalization rate and infection fatality rate were estimated to be 6.86% and 0.95%, respectively, among community residents in Connecticut., (Published by Elsevier Inc.)

It is essential to study the viral droplet's uptake in the human respiratory system to better control, prevent, and treat diseases. Micro-droplets can easily pass through ordinary respiratory masks. Therefore, the SARS-COV-2 transmit easily in conversation with a regular mask with 'silent spreaders' in the most physiological way of breathing through the nose, indoor and at rest condition. The results showed that the amount of deposited micro-droplets in the olfactory epithelium area is low. Also, due to receptors and long droplet residence time in this region, the possibility of absorption increases in the cribriform plate. This phenomenon eventually could lead to brain lesion damage and, in some cases, leads to stroke. In all inlet flow rates lower than 30 L/min inlet boundary conditions, the average percentage of viral contamination for upper respiratory tract is always less than 50% and more than 50% for the lungs. At 6L/min and 15L/min flow rates, the average percentage of lung contamination increases to more than 87%, which due to the presence of the Coronavirus receptor in the lungs, the involvement of the lungs increases significantly. This study's other achievements include the inverse relationship between droplets deposition efficiency in some parts of the upper airway, which have the most deformation in the tract. Also, the increased deformities per minute applied to the trachea and nasal cavity, which is 1.5 times more than usual, could lead to chest and head bothers.

It is of critical importance to estimate changing disease-transmission rates and their dependence on population mobility. A common approach to this problem involves fitting daily transmission rates using a susceptible-exposed-infected-recovered-(SEIR) model (regularizing to avoid overfitting) and then computing the relationship between the estimated transmission rate and mobility. Unfortunately, there are often several very different transmission-rate trajectories that can fit the reported cases well, meaning that the choice of regularization determines the final solution (and thus the mobility-transmission rate relationship) selected by the SEIR model. Moreover, the classical approaches to regularization-penalizing the derivative of the transmission rate trajectory-do not correspond to realistic properties of pandemic spread. Consequently, models fitted using derivative-based regularization are often biased toward underestimating the current transmission rate and future deaths. In this work, we propose mobility-driven regularization of the SEIR transmission rate trajectory. This method rectifies the artificial regularization problem, produces more accurate and unbiased forecasts of future deaths, and estimates a highly interpretable relationship between mobility and the transmission rate. For this analysis, mobility data related to the coronavirus disease 2019 pandemic was collected by Safegraph (San Francisco, California) from major US cities between March and August 2020., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)