Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study

Cellular and molecular features of COVID-19 associated ARDS: therapeutic relevance

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic or cause a disease (COVID-19) characterized by different levels of severity. The main cause of severe COVID-19 and death is represented by acute (or acute on chronic) respiratory failure and acute respiratory distress syndrome (ARDS), often requiring hospital admission and ventilator support.The molecular pathogenesis of COVID-19-related ARDS (by now termed c-ARDS) is still poorly understood. In this review we will discuss the genetic susceptibility to COVID-19, the pathogenesis and the local and systemic biomarkers correlated with c-ARDS and the therapeutic options that target the cell signalling pathways of c-ARDS.

Co-administration of AYUSH 64 as an adjunct to standard of care in mild and moderate COVID-19: A randomized, controlled, multicentric clinical trial

OBJECTIVE

Evaluate the efficacy of AYUSH 64, a standard polyherbal Ayurvedic drug in COVID-19.

METHODS

During the first pandemic wave, 140 consenting and eligible hospitalized adult participants with mild-moderate symptomatic disease (specific standard RT-PCR assay positive) were selected as per a convenience sample, and randomized (1:1 ratio) to an open-label (assessor blind) two-arm multicentric drug trial; standard of care (SOC as per Indian guidelines) versus AYUSH 64 combined with SOC (AYUSH plus). Participants were assessed daily and discharged once clinical recovery (CR, primary efficacy) was achieved which was based on a predetermined set of criteria (resolution of symptoms, normal peripheral oximetry, and negative specific RT-PCR assay). Each participant was followed using an indigenous software program(mobile phone) and completed a 12-week study period. The dose of AYUSH 64 was 2 tablets oral, 500 mg each, bid for 12 weeks (AYUSH plus only). Significant P was <0.05 (two-sided). On randomization, the groups were found well matched.

RESULTS

The mean interval time from randomization to CR was significantly superior in the AYUSH plus group [mean 6.45 days versus 8.26 days, 95% Confidence Interval of the difference -3.02 to -0.59 (P = 0.003, Student's 't test] as per-protocol analysis (134 participants); significant (P = 0.002) on an intention to treat analysis. 70% of the participants in AYUSH plus recovered during the first week (P = 0.046, Chi-square) and showed a significantly better change in physical health, fatigue, and quality of life measures. 48 adverse events, mostly mild and gut related, were reported by each group. There were 20 patient withdrawals (8 in AYUSH plus) but none due to an AE. There were no deaths. Daily assessment (hospitalization) and supervised drug intake ensured robust efficacy data. The open-label design was a concern (study outcome).

CONCLUSIONS

AYUSH 64 in combination with SOC hastened recovery, reduced hospitalization, and improved health in COVID-19. It was considered safe and well-tolerated. Further clinical validation (Phase III) is required.

TRIAL REGISTRATION

CTRI/2020/06/025557.

Assessing the impacts of COVID-19 vaccination programme's timing and speed on health benefits, cost-effectiveness, and relative affordability in 27 African countries

BACKGROUND

The COVID-19 vaccine supply shortage in 2021 constrained roll-out efforts in Africa while populations experienced waves of epidemics. As supply improves, a key question is whether vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.

METHODS

We assessed the impact of vaccination programme timing using an epidemiological and economic model. We fitted an age-specific dynamic transmission model to reported COVID-19 deaths in 27 African countries to approximate existing immunity resulting from infection before substantial vaccine roll-out. We then projected health outcomes (from symptomatic cases to overall disability-adjusted life years (DALYs) averted) for different programme start dates (01 January to 01 December 2021, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/million population-day, respectively) for viral vector and mRNA vaccines by the end of 2022. Roll-out rates used were derived from observed uptake trajectories in this region. Vaccination programmes were assumed to prioritise those above 60 years before other adults. We collected data on vaccine delivery costs, calculated incremental cost-effectiveness ratios (ICERs) compared to no vaccine use, and compared these ICERs to GDP per capita. We additionally calculated a relative affordability measure of vaccination programmes to assess potential nonmarginal budget impacts.

RESULTS

Vaccination programmes with early start dates yielded the most health benefits and lowest ICERs compared to those with late starts. While producing the most health benefits, fast vaccine roll-out did not always result in the lowest ICERs. The highest marginal effectiveness within vaccination programmes was found among older adults. High country income groups, high proportions of populations over 60 years or non-susceptible at the start of vaccination programmes are associated with low ICERs relative to GDP per capita. Most vaccination programmes with small ICERs relative to GDP per capita were also relatively affordable.

CONCLUSION

Although ICERs increased significantly as vaccination programmes were delayed, programmes starting late in 2021 may still generate low ICERs and manageable affordability measures. Looking forward, lower vaccine purchasing costs and vaccines with improved efficacies can help increase the economic value of COVID-19 vaccination programmes.

A Method of Estimating Time-to-Recovery for a Disease Caused by a Contagious Pathogen Such as SARS-CoV-2 Using a Time Series of Aggregated Case Reports

During the outbreak of a disease caused by a pathogen with unknown characteristics, the uncertainty of its progression parameters can be reduced by devising methods that, based on rational assumptions, exploit available information to provide actionable insights. In this study, performed a few (~6) weeks into the outbreak of COVID-19 (caused by SARS-CoV-2), one of the most important disease parameters, the average time-to-recovery, was calculated using data publicly available on the internet (daily reported cases of confirmed infections, deaths, and recoveries), and fed into an algorithm that matches confirmed cases with deaths and recoveries. Unmatched cases were adjusted based on the matched cases calculation. The mean time-to-recovery, calculated from all globally reported cases, was found to be 18.01 days (SD 3.31 days) for the matched cases and 18.29 days (SD 2.73 days) taking into consideration the adjusted unmatched cases as well. The proposed method used limited data and provided experimental results in the same region as clinical studies published several months later. This indicates that the proposed method, combined with expert knowledge and informed calculated assumptions, could provide a meaningful calculated average time-to-recovery figure, which can be used as an evidence-based estimation to support containment and mitigation policy decisions, even at the very early stages of an outbreak.

Wastewater-based prediction of COVID-19 cases using a highly sensitive SARS-CoV-2 RNA detection method combined with mathematical modeling

Wastewater-based epidemiology (WBE) has the potential to predict COVID-19 cases; however, reliable methods for tracking SARS-CoV-2 RNA concentrations (CRNA) in wastewater are lacking. In the present study, we developed a highly sensitive method (EPISENS-M) employing adsorption-extraction, followed by one-step RT-Preamp and qPCR. The EPISENS-M allowed SARS-CoV-2 RNA detection from wastewater at 50 % detection rate when newly reported COVID-19 cases exceed 0.69/100,000 inhabitants in a sewer catchment. Using the EPISENS-M, a longitudinal WBE study was conducted between 28 May 2020 and 16 June 2022 in Sapporo City, Japan, revealing a strong correlation (Pearson's r = 0.94) between CRNA and the newly COVID-19 cases reported by intensive clinical surveillance. Based on this dataset, a mathematical model was developed based on viral shedding dynamics to estimate the newly reported cases using CRNA data and recent clinical data prior to sampling day. This developed model succeeded in predicting the cumulative number of newly reported cases after 5 days of sampling day within a factor of √2 and 2 with a precision of 36 % (16/44) and 64 % (28/44), respectively. By applying this model framework, another estimation mode was developed without the recent clinical data, which successfully predicted the number of COVID-19 cases for the succeeding 5 days within a factor of √2 and 2 with a precision of 39 % (17/44) and 66 % (29/44), respectively. These results demonstrated that the EPISENS-M method combined with the mathematical model can be a powerful tool for predicting COVID-19 cases, especially in the absence of intensive clinical surveillance.

Stochastic simulation of successive waves of COVID-19 in the province of Barcelona

Analytic compartmental models are currently used in mathematical epidemiology to forecast the COVID-19 pandemic evolution and explore the impact of mitigation strategies. In general, such models treat the population as a single entity, losing the social, cultural and economical specificities. We present a network model that uses socio-demographic datasets with the highest available granularity to predict the spread of COVID-19 in the province of Barcelona. The model is flexible enough to incorporate the effect of containment policies, such as lockdowns or the use of protective masks, and can be easily adapted to future epidemics. We follow a stochastic approach that combines a compartmental model with detailed individual microdata from the population census, including social determinants and age-dependent strata, and time-dependent mobility information. We show that our model reproduces the dynamical features of the disease across two waves and demonstrates its capability to become a powerful tool for simulating epidemic events.

Functional Textile Materials for Blocking COVID-19 Transmission

The outbreak of COVID-19 provided a warning sign for society worldwide: that is, we urgently need to explore effective strategies for combating unpredictable viral pandemics. Protective textiles such as surgery masks have played an important role in the mitigation of the COVID-19 pandemic, while revealing serious challenges in terms of supply, cross-infection risk, and environmental pollution. In this context, textiles with an antivirus functionality have attracted increasing attention, and many innovative proposals with exciting commercial possibilities have been reported over the past three years. In this review, we illustrate the progress of textile filtration for pandemics and summarize the recent development of antiviral textiles for personal protective purposes by cataloging them into three classes: metal-based, carbon-based, and polymer-based materials. We focused on the preparation routes of emerging antiviral textiles, providing a forward-looking perspective on their opportunities and challenges, to evaluate their efficacy, scale up their manufacturing processes, and expand their high-volume applications. Based on this review, we conclude that ideal antiviral textiles are characterized by a high filtration efficiency, reliable antiviral effect, long storage life, and recyclability. The expected manufacturing processes should be economically feasible, scalable, and quickly responsive.

Persuasive Messages for Improving Adherence to COVID-19 Prevention Behaviors: Randomized Online Experiment

BACKGROUND

Adherence to nonpharmaceutical interventions for COVID-19, including physical distancing, masking, staying home while sick, and avoiding crowded indoor spaces, remains critical for limiting the spread of COVID-19.

OBJECTIVE

The aim of this study was to test the effectiveness of using various persuasive appeals (deontological moral frame, empathy, identifiable victim, goal proximity, and reciprocity) at improving intentions to adhere to prevention behaviors.

METHODS

A randomized online experiment using a representative sample of adult Canadian residents with respect to age, ethnicity, and province of residence was performed from March 3 to March 6, 2021. Participants indicated their intentions to follow public health guidelines, saw one of six flyers featuring a persuasive appeal or no appeal, and then rated their intentions a second time. Known correlates of attitudes toward public health measures were also measured.

RESULTS

Intentions to adhere to public health measures increased in all appeal conditions. The message featuring an empathy appeal resulted in a greater increase in intentions than the control (no appeal) message. Moreover, the effectiveness of persuasive appeals was moderated by baseline intentions. Deontological, empathy, identifiable victim, and reciprocity appeals improved intentions more than the control message, but only for people with lower baseline intentions to adhere to nonpharmaceutical interventions.

CONCLUSIONS

Public health marketing campaigns aiming to increase adherence to COVID-19 protective behaviors could achieve modest gains by employing a range of persuasive appeals. However, to maximize impact, it is important that these campaigns be targeted to the right individuals.

TRIAL REGISTRATION

ClinicalTrials.gov NCT05722106; https://clinicaltrials.gov/ct2/show/NCT05722106.

Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations

BACKGROUND

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible in vaccinated and unvaccinated populations. The dynamics that govern its establishment and propensity toward fixation (reaching 100% frequency in the SARS-CoV-2 population) in communities remain unknown. Here, we describe the dynamics of Omicron at 3 institutions of higher education (IHEs) in the greater Boston area.

METHODS

We use diagnostic and variant-specifying molecular assays and epidemiological analytical approaches to describe the rapid dominance of Omicron following its introduction into 3 IHEs with asymptomatic surveillance programs.

RESULTS

We show that the establishment of Omicron at IHEs precedes that of the state and region and that the time to fixation is shorter at IHEs (9.5-12.5 days) than in the state (14.8 days) or region. We show that the trajectory of Omicron fixation among university employees resembles that of students, with a 2- to 3-day delay. Finally, we compare cycle threshold values in Omicron vs Delta variant cases on college campuses and identify lower viral loads among college affiliates who harbor Omicron infections.

CONCLUSIONS

We document the rapid takeover of the Omicron variant at IHEs, reaching near-fixation within the span of 9.5-12.5 days despite lower viral loads, on average, than the previously dominant Delta variant. These findings highlight the transmissibility of Omicron, its propensity to rapidly dominate small populations, and the ability of robust asymptomatic surveillance programs to offer early insights into the dynamics of pathogen arrival and spread.

Identifying High-Risk Events for COVID-19 Transmission: Estimating the Risk of Clustering Using Nationwide Data

The transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to be overdispersed, meaning that only a fraction of infected cases contributes to super-spreading. While cluster interventions are an effective measure for controlling pandemics due to the viruses' overdispersed nature, a quantitative assessment of the risk of clustering has yet to be sufficiently presented. Using systematically collected cluster surveillance data for coronavirus disease 2019 (COVID-19) from June 2020 to June 2021 in Japan, we estimated the activity-dependent risk of clustering in 23 establishment types. The analysis indicated that elderly care facilities, welfare facilities for people with disabilities, and hospitals had the highest risk of clustering, with 4.65 (95% confidence interval [CI]: 4.43-4.87), 2.99 (2.59-3.46), and 2.00 (1.88-2.12) cluster reports per million event users, respectively. Risks in educational settings were higher overall among older age groups, potentially being affected by activities with close and uncontrollable contact during extracurricular hours. In dining settings, drinking and singing increased the risk by 10- to 70-fold compared with regular eating settings. The comprehensive analysis of the COVID-19 cluster records provides an additional scientific basis for the design of customized interventions.

The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021

Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.

Community pandemic prevention and control measures and their influence on citizen satisfaction during the COVID-19 pandemic in China

At the forefront of the fight against the pandemic, the community' s measures and services would have a greater impact than ever before on citizen satisfaction. However, the influence of citizen satisfaction on community pandemic prevention and control measures (CPPCM) during the pandemic is poorly understood. This study aims to investigate the allocation of CPPCM and its impact on CS. The Chinese national data was analyzed for the outcome. (1) Pandemic prevention propaganda (PPP), disinfection (DT), and body temperature tests (BTTs) were the primary measures taken by the Chinese community. (2) The CS for pandemic prevention and control is high, and urban and central Chinese communities express greater satisfaction. (3) The impact of disinfection, body temperature tests, free supplies, and assistance purchasing supplies on CS was greater in rural areas than in urban areas. (4) Regional variations exist in the impact of CS on CPPCM. (5) The number of measures has an inverted U-shaped relationship with citizen satisfaction. This study also suggests that the government should disseminate information about pandemic prevention in a timely manner, provide basic health and medical services, and evaluate the measures taken to avoid the discount effect.

Application of big data and artificial intelligence in epidemic surveillance and containment

Faced with the current time-sensitive COVID-19 pandemic, the overburdened healthcare systems have resulted in a strong demand to develop newer methods to control the spread of the pandemic. Big data and artificial intelligence (AI) have been leveraged amid the COVID-19 pandemic; however, little is known about their use for supporting public health efforts. In epidemic surveillance and containment, efforts are needed to treat critical patients, track and manage the health status of residents, isolate suspected cases, and develop vaccines and antiviral drugs. The applications of emerging practices of artificial intelligence and big data have become powerful "weapons" to fight against the pandemic and provide strong support in pandemic prevention and control, such as early warning, analysis and judgment, interruption and intervention of epidemic, to achieve goals of early detection, early report, early diagnosis, early isolation and early treatment. These are the decisive factors to control the spread of the epidemic and reduce the mortality. This paper systematically summarized the application of big data and AI in epidemic, and describes practical cases and challenges with emphasis on epidemic prevention and control. The included studies showed that big data and AI have the potential strength to fight against COVID-19. However, many of the proposed methods are not yet widely accepted. Thus, the most rewarding research would be on methods that promise value beyond COVID-19. More efforts are needed for developing standardized reporting protocols or guidelines for practice.

A general urban spreading pattern of COVID-19 and its underlying mechanism

Currently, the global situation of COVID-19 is aggravating, pressingly calling for efficient control and prevention measures. Understanding the spreading pattern of COVID-19 has been widely recognized as a vital step for implementing non-pharmaceutical measures. Previous studies explained the differences in contagion rates due to the urban socio-political measures, while fine-grained geographic urban spreading pattern still remains an open issue. Here, we fill this gap by leveraging the trajectory data of 197,808 smartphone users (including 17,808 anonymous confirmed cases) in nine cities in China. We find a general spreading pattern in all cities: the spatial distribution of confirmed cases follows a power-law-like model and the spreading centroid human mobility is time-invariant. Moreover, we reveal that long average traveling distance results in a high growth rate of spreading radius and wide spatial diffusion of confirmed cases in the fine-grained geographic model. With such insight, we adopt the Kendall model to simulate the urban spreading of COVID-19 which can well fit the real spreading process. Our results unveil the underlying mechanism behind the spatial-temporal urban evolution of COVID-19, and can be used to evaluate the performance of mobility restriction policies implemented by many governments and to estimate the evolving spreading situation of COVID-19.

Association between COVID-19 risk-mitigation behaviors and specific mental disorders in youth

BACKGROUND

Although studies of adults show that pre-existing mental disorders increase risk for COVID-19 infection and severity, there is limited information about this association among youth. Mental disorders in general as well as specific types of disorders may influence the ability to comply with risk-mitigation strategies to reduce COVID-19 infection and transmission.

METHODS

Youth compliance (rated as "Never," "Sometimes," "Often," or "Very often/Always") with risk mitigation was reported by parents on the CoRonavIruS Health Impact Survey (CRISIS) in January 2021. The sample comprised 314 female and 514 male participants from the large-scale Child Mind Institute Healthy Brain Network, a transdiagnostic self-referred, community sample of children and adolescents (ages 5-21). Responses were summarized using factor analysis of risk mitigation, and their associations with lifetime mental disorders (assessed via structured diagnostic interviews) were identified with linear regression analyses (adjusted for covariates). All analyses used R Project for Statistical Computing for Mac (v.4.0.5).

RESULTS

A two-factor model was the best-fitting solution. Factor 1 (avoidance behaviors) included avoiding groups, indoor settings, and other peoples' homes; avoidance scores were higher among youth with any anxiety disorder (p = .01). Factor 2 (hygiene behaviors) included using hand sanitizer, washing hands, and maintaining social distance; hygiene scores were lower among youth with ADHD (combined type) (p = .02). Mask wearing was common (90%), did not load on either factor, and was not associated with any mental health disorder.

CONCLUSION AND RELEVANCE

Although most mental disorders examined were not associated with risk mitigation, youth with ADHD characterized by hyperactivity plus inattention may need additional support to consistently engage in risk-mitigation behaviors. Enhancing risk-mitigation strategies among at-risk groups of youth may help reduce COVID-19 infection and transmission.

Modeling and Global Sensitivity Analysis of Strategies to Mitigate Covid-19 Transmission on a Structured College Campus

In response to the COVID-19 pandemic, many higher educational institutions moved their courses on-line in hopes of slowing disease spread. The advent of multiple highly-effective vaccines offers the promise of a return to "normal" in-person operations, but it is not clear if-or for how long-campuses should employ non-pharmaceutical interventions such as requiring masks or capping the size of in-person courses. In this study, we develop and fine-tune a model of COVID-19 spread to UC Merced's student and faculty population. We perform a global sensitivity analysis to consider how both pharmaceutical and non-pharmaceutical interventions impact disease spread. Our work reveals that vaccines alone may not be sufficient to eradicate disease dynamics and that significant contact with an infectious surrounding community will maintain infections on-campus. Our work provides a foundation for higher-education planning allowing campuses to balance the benefits of in-person instruction with the ability to quarantine/isolate infectious individuals.

COVID-19 coronavirus infection in children: Clinical presentation, diagnosis, vaccination, and treatment

In late 2019, a new subtype of coronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19 SARS-CoV-2) rapidly spread around the world, causing a global pandemic. Initially, the proportion of confirmed cases among children was relatively small, and it was believed that children were rarely infected. Subsequent observations have shown that in children and adolescents, the infection is either asymptomatic or paucisymptomatic, and therefore the true incidence is underestimated due to the lack of testing. The article systematizes the results of studies on the prevalence, diagnosis, clinical features, vaccination, and treatment of children with a new coronavirus infection COVID-19 SARS-CoV-2. The SARS-CoV-2 positivity rate throughout the peak of the pandemic in children was low compared to adults. Children are not only less likely to become infected with the virus, but they also endure the infection more easily than adults. The mortality rate in children with COVID-19 was <0.5%. In most children, infection is either asymptomatic or paucisymptomatic. Vaccination of children and adolescents is recommended mainly to achieve herd immunity in all age groups. However, there are no convincing data on the duration of the immune response, the level of the required protective antibody titer, as well as on the long-term side effects of vaccination due to the insufficient follow-up period and the uncertainty of the immune response criteria. As information is accumulated on the viral load of children and adolescents, their role in the transmission of the virus, diagnostic approaches in this age group are optimized. The effectiveness of the treatment was tested on patients admitted to the hospital, and recommendations for treatment were developed. Currently, global research efforts are focused on the protection of particularly vulnerable children, the prospects for total childhood vaccination, its effectiveness and safety.

Utilizing student-led contact tracing initiative to alleviate COVID-19 disease burden in central Pennsylvania

PURPOSE

Contact tracing elicits probable contacts from COVID-19 cases. Our student-led contact tracing initiative promoted isolation of both confirmed and probable cases and quarantine of contacts to reduce disease in Central Pennsylvania.

METHODS

Close contacts of COVID-19 cases were contacted by tracers, advised to quarantine, and monitored for 14 days for symptoms. Symptomatic contacts were classified as probable cases and advised to isolate. Data was collected from March 24, 2020 to May 26, 2020. Poisson regression and linear regression were utilized to examine the relationships between case and number of contacts and proportion of symptomatic contacts.

RESULTS

Study sample comprised of 346 confirmed and 157 probable cases. Our results indicate a significant difference in percent of household contacts who became symptomatic between confirmed and probable cases (22% vs. 3%; adjusted P<.01). Similarly, probable cases had significantly fewer non-household contacts compared to confirmed cases (0.87 vs. 0.55; adjusted P<.01).

CONCLUSIONS

Timely notification of exposure to a COVID-19 positive individual by student contact tracers allowed for probable cases to quarantine early in the disease process. Our data suggests that early quarantine and/or isolation may have directly contributed to probable cases having fewer non-household contacts and a smaller proportion of symptomatic household-contacts compared to confirmed cases.

Evaluation of depression, anxiety and posttraumatic stress response levels of children and adolescents treated with COVID-19

We aimed to evaluate stress level reactions to depression, anxiety, and posttraumatic stress in paediatric patients' post-COVID-19 infection. A total of two hundred consecutive patients aged 8 to 18 years were prospectively enrolled in the study between March 2020 and June 2021. One hundred patients were diagnosed with a positive COVID-PCR test and had inpatient management. Another hundred patients had positive COVID-PCR results and completed their care and isolation for 14 days at home. We used the child posttraumatic stress reaction index (CPTS-RI), child depression inventory (CDI), and screen for child anxiety-related disorders (SCARED) to evaluate their post-COVID-19 infection mental health state. In the study population, the mean age was 13.4 years, and 50.5% were male. Sixty-seven patients were paediatric, and the rest were adolescents. Based on our scaling system, 10% of patients had depression. Forty-one percent of patients had at least one high subscale of SCARED. Forty-four percent of patients' CPTS-RI was above the normal limit, while 4% had a severe stress reaction level. In the female patient population, SCARED and CPTS-RI were significantly high (p = 0.01). There was no significant correlation between hospitalization duration and test scores. The CPTS-RI score was significantly higher in the outpatient group than in the other groups (p = 0.01). The inpatient group had significantly higher social phobia, while the outpatient group had significantly higher school phobia (p = 0.01 and p = 0.05, respectively).

CONCLUSION

The present study showed that COVID-19 infection is a significant risk factor for psychopathology in children and adolescents.

WHAT IS KNOWN

• COVID-19 causes multiple physical complications in the body along with significant harmful physiologic mental health effects. After being diagnosed with COVID-19, paediatric and adolescent patients have been engaging in social isolation. • Shutdowns, school closings, minimizing social interaction, and isolating behaviour are some of the measures used to control the pandemic. For kids to develop into healthy individuals, they need social interaction and a safe environment.

WHAT IS NEW

• The present study showed that COVID-19 infection is a significant risk factor for childhood and adolescent psychopathology. Based on our scaling system, 10% of patients had depression. Forty-four percent of patients' CPTS-RI was above the normal limit, while 4% had a severe stress reaction level. In the female patient population, SCARED and CPTS-RI were significantly high. • These patients need to be evaluated and monitored by paediatric and adolescent psychiatry clinics simultaneously with paediatric clinics.

Age-specific SARS-CoV-2 infection fatality rates derived from serological data vary with income and income inequality

The ongoing COVID-19 pandemic has killed at least 1.1 million people in the United States and over 6.7 million globally. Accurately estimating the age-specific infection fatality rate (IFR) of SARS-CoV-2 for different populations is crucial for assessing and understanding the impact of COVID-19 and for appropriately allocating vaccines and treatments to at-risk groups. We estimated age-specific IFRs of wild-type SARS-CoV-2 using published seroprevalence, case, and death data from New York City (NYC) from March to May 2020, using a Bayesian framework that accounted for delays between key epidemiological events. IFRs increased 3-4-fold with every 20 years of age, from 0.06% in individuals between 18-45 years old to 4.7% in individuals over 75. We then compared IFRs in NYC to several city- and country-wide estimates including England, Switzerland (Geneva), Sweden (Stockholm), Belgium, Mexico, and Brazil, as well as a global estimate. IFRs in NYC were higher for individuals younger than 65 years old than most other populations, but similar for older individuals. IFRs for age groups less than 65 decreased with income and increased with income inequality measured using the Gini index. These results demonstrate that the age-specific fatality of COVID-19 differs among developed countries and raises questions about factors underlying these differences, including underlying health conditions and healthcare access.

Association Between Population-Level Factors and Household Secondary Attack Rate of SARS-CoV-2: A Systematic Review and Meta-analysis

Background

Accurate estimation of household secondary attack rate (SAR) is crucial to understand the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The impact of population-level factors, such as transmission intensity in the community, on SAR estimates is rarely explored.

Methods

In this study, we included articles with original data to compute the household SAR. To determine the impact of transmission intensity in the community on household SAR estimates, we explored the association between SAR estimates and the incidence rate of cases by country during the study period.

Results

We identified 163 studies to extract data on SARs from 326 031 cases and 2 009 859 household contacts. The correlation between the incidence rate of cases during the study period and SAR estimates was 0.37 (95% CI, 0.24-0.49). We found that doubling the incidence rate of cases during the study period was associated with a 1.2% (95% CI, 0.5%-1.8%) higher household SAR.

Conclusions

Our findings suggest that the incidence rate of cases during the study period is associated with higher SAR. Ignoring this factor may overestimate SARs, especially for regions with high incidences, which further impacts control policies and epidemiological characterization of emerging variants.

Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: A prospective comparative clinical trial

BACKGROUND

Nasopharyngeal antigen Rapid Diagnostic Tests (RDTs), saliva RT-PCR and nasopharyngeal (NP) RT-PCR have shown different performance characteristics to detect patients infected by SARS-CoV-2, according to the viral load (VL)-and thus transmissibility.

METHODS

In October 2020, we conducted a prospective trial involving patients presenting at testing centres with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR, according to VL and symptoms duration.

RESULTS

Out of 949 patients enrolled, 928 patients had all three tests performed. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) ≥106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively. Sensitivity of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients, 94.5% (91.5-96.7%) for those with VL≥105 and 96.5% (93.6-98.3%) for those with VL≥106. Sensitivity of STANDARD-Q®, Panbio™ and COVID-VIRO® Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL≥106, sensitivity was 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. No patient with VL<104 was detected by RDT. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%, 83.5-91.3%) and ≥4 days (85.7%, 75.9-92.6%) after symptoms onset (p = 0.6). Sensitivity of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR.

CONCLUSIONS

RDT results allow rapid identification of COVID cases with immediate isolation of most contagious individuals. RDT can thus be a game changer both in ambulatory care and community testing aimed at stopping transmission chains, and even more so in resource-constrained settings thanks to its very low price. When PCR is performed, saliva could replace NP swabbing.

TRIAL REGISTRATION

ClinicalTrial.gov Identifier: NCT04613310 (03/11/2020).

Magnetic Resonance Imaging Scan of the Brain After Mild COVID-19 Infection

PURPOSE

There have been several reports of central nervous system impairments associated with severe coronavirus disease 2019 (COVID-19) infection on head magnetic resonance imaging and angiography (MRI/A). However, head MRI/A is rarely performed in mild cases, and there have been few reports on intracranial changes after COVID-19 infection in these cases. Here, we report a comparative examination of the findings seen in common head MRI/A sequences in mild cases of COVID-19.

METHODS

Of the 15,376 patients who underwent head MRI/A examination called "Brain Dock" between June 2020 and June 2021, 746 patients who received a COVID-19 antibody test were evaluated. Positive and negative patients were comparatively examined for head MRI/A findings such as cerebral white matter lesions, ischemic changes, cerebral microbleeds, cerebral aneurysms, arterial stenosis, sinusitis, and other abnormal findings.

RESULTS

Overall, 31 (4.2%) patients were COVID-19 positive, and all of them had mild infections not requiring hospitalization. There was no significant difference in patient characteristics and head MRI/A findings between positive and negative patients. All positive patients showed no particular abnormalities in the nasal findings such as olfactory bulb atrophy or thickening of the olfactory mucosa.

CONCLUSION

Intracranial lesions in mild patients do not show a clear difference from those in negative patients. This indicates that findings seen in common MRI/A sequences of severe patients are not likely in mild patients, supporting that there is relatively no damage to the central nervous system in mild patients.

Coupling the Within-Host Process and Between-Host Transmission of COVID-19 Suggests Vaccination and School Closures are Critical

Most models of COVID-19 are implemented at a single micro or macro scale, ignoring the interplay between immune response, viral dynamics, individual infectiousness and epidemiological contact networks. Here we develop a data-driven model linking the within-host viral dynamics to the between-host transmission dynamics on a multilayer contact network to investigate the potential factors driving transmission dynamics and to inform how school closures and antiviral treatment can influence the epidemic. Using multi-source data, we initially determine the viral dynamics and estimate the relationship between viral load and infectiousness. Then, we embed the viral dynamics model into a four-layer contact network and formulate an agent-based model to simulate between-host transmission. The results illustrate that the heterogeneity of immune response between children and adults and between vaccinated and unvaccinated infections can produce different transmission patterns. We find that school closures play a significant effect on mitigating the pandemic as more adults get vaccinated and the virus mutates. If enough infected individuals are diagnosed by testing before symptom onset and then treated quickly, the transmission can be effectively curbed. Our multiscale model reveals the critical role played by younger individuals and antiviral treatment with testing in controlling the epidemic.

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

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

Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework

BACKGROUND

Universities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University and introduce a SARS-CoV-2 surveillance and response framework.

METHODS

We analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and WiFi-based co-location data) alongside pathogen surveillance data (wastewater and diagnostic testing, and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy. We applied relative risk, multiple linear regression, and social network assortativity to identify attributes or behaviors associated with contracting SARS-CoV-2. To characterize SARS-CoV-2 transmission, we used viral sequencing, phylogenomic tools, and functional assays.

FINDINGS

Athletes, particularly those on high-contact teams, had the highest risk of testing positive. On average, individuals who tested positive had more contacts and longer interaction durations than individuals who never tested positive. The distribution of contacts per individual was overdispersed, although not as overdispersed as the distribution of phylogenomic descendants. Corroboration via technical replicates was essential for identification of wastewater mutations.

CONCLUSIONS

Based on our findings, we formulate a framework that combines tools into an integrated disease surveillance program that can be implemented in other congregate settings with limited resources.

FUNDING

This work was supported by the National Science Foundation, the Hertz Foundation, the National Institutes of Health, the Centers for Disease Control and Prevention, the Massachusetts Consortium on Pathogen Readiness, the Howard Hughes Medical Institute, the Flu Lab, and the Audacious Project.

Epidemiological characteristics and quarantine assessment of imported international COVID-19 cases, March to December 2020, Chengdu, China

International flights have accelerated the global spread of Coronavirus Disease 2019 (COVID-19). Determination of the optimal quarantine period for international travelers is crucial to prevent the local spread caused by imported COVID-19 cases. We performed a retrospective epidemiological study using 491 imported COVID-19 cases in Chengdu, China, to describe the characteristic of the cases and estimate the time from arrival to confirmation for international travelers using nonparametric survival methods. Among the 491 imported COVID-19 cases, 194 (39.5%) were asymptomatic infections. The mean age was 35.6 years (SD = 12.1 years) and 83.3% were men. The majority (74.1%) were screened positive for SARS-CoV-2, conducted by Chengdu Customs District, the People's Republic of China. Asymptomatic cases were younger than presymptomatic or symptomatic cases (P < 0.01). The daily number of imported COVID-19 cases displayed jagged changes. 95% of COVID-19 cases were confirmed by PT-PCR within 14 days (95% CI 13-15) after arriving in Chengdu. A 14-day quarantine measure can ensure non-infection among international travelers with a 95% probability. Policymakers may consider an extension of the quarantine period to minimize the negative consequences of the COVID-19 confinement and prevent the international spread of COVID-19. Nevertheless, the government should consider the balance between COVID-19 and socioeconomic development, which may cause more serious social and health crises.

The Implementation of a Health Care Worker Screening Program Based on the Advanta RT-qPCR Saliva Assay in a Tertiary Care Referral Hospital in Northern Greece

Health care workers are at increased risk of acquiring SARS-CoV-2 infection due to different exposures in the community and in hospital settings. Interventions implemented to avoid nosocomial outbreaks include preventive testing strategies. In this report, we present results from the mass screening program applied in our hospital to all professionals, irrespective of symptoms or risk of exposure. We processed saliva specimens with real-time reverse transcription polymerase chain reaction. The total number of samples received was 43,726. Positive results were 672 and average positivity rate was 1.21%. The average positivity rate was similar to the positivity rate in the community in Greece and EU. More specifically, 80.5% of the positive participants care for patients in their daily activities, 31% experienced no symptoms before receiving the positive result, 46.1% reported a close contact with a patient or infected coworkers and 32.8% reported a close contact with infected family members. We believe that the identification of asymptomatic carriers has proved the effectiveness of the screening program by preventing the putative nosocomial spread of the virus and the depletion of workforce. In conclusion, in times of high incidence in the community, the periodic testing of health care personnel is wise and relevant for implementation costs.

COVID-19 in one region of New Zealand: a descriptive epidemiological study

OBJECTIVE

To describe the epidemiology of COVID-19 in one region of New Zealand in the context of the national lockdown and provide a reference for comparing infection dynamics and control measures between SARS-Cov-2 strains.  Methods: Epidemiological linking and analysis of COVID-19 cases and their close contacts residing in the geographical area served by the Southern District Health Board (SDHB).  Results: From 13 March to 5 April 5 2020, 186 cases were laboratory-confirmed with wild-type Sars-Cov-2 in SDHB. Overall, 35·1% of cases were attributable to household transmission, 27·0% to non-household, 25·4% to overseas travel and 12·4% had no known epidemiological links. The highest secondary attack rate was observed in households during lockdown (15·3%, 95%CI 10·4-21·5). The mean serial interval in 50 exclusive infector-infectee pairs was 4·0 days (95%CI 3·2-4·7days), and the mean incubation period was 3.4 days (95%CI 2·7-4·2).

CONCLUSIONS

The SARS-CoV-2 incubation period may be shorter than early estimates that were limited by uncertainties in exposure history or small sample sizes.

IMPLICATIONS FOR PUBLIC HEALTH

The continuation of household transmission during lockdown highlights the need for effective home-based quarantine guidance. Our findings of a short incubation period highlight the need to contact trace and isolate as rapidly as possible.

Use of surveillance data to elucidate household clustering of SARS-CoV-2 in Fulton County, Georgia a major metropolitan area

BACKGROUND

Households are important for SARS-CoV-2 transmission due to high intensity exposure in enclosed spaces over prolonged durations. We quantified and characterized household clustering of COVID-19 cases in Fulton County, Georgia.

METHODS

We used surveillance data to identify all confirmed COVID-19 cases in Fulton County. Household clustered cases were defined as cases with matching residential address. We described the proportion of COVID-19 cases that were clustered, stratified by age over time and explore trends in age of first diagnosed case within households and subsequent household cases.

RESULTS

Between June 1, 2020 and October 31, 2021, 31,449(37%) of 106,233 cases were clustered in households. Children were the most likely to be in household clusters than any other age group. Initially, children were rarely (∼ 10%) the first cases diagnosed in the household but increased to almost 1 of 3 in later periods.

DISCUSSION

One-third of COVID-19 cases in Fulton County were part of a household cluster. Increasingly children were the first diagnosed case, coinciding with temporal trends in vaccine roll-out among the elderly and the return to in-person schooling in Fall 2021. Limitations include restrictions to cases with a valid address and unit number and that the first diagnosed case may not be the infection source for the household.

Understanding the impact of rapid antigen tests on SARS-CoV-2 transmission in the fifth wave of COVID-19 in Hong Kong in early 2022

The fast-spreading Omicron variant of SARS-CoV-2 overwhelmed Hong Kong, causing the fifth wave of COVID-19. It remains to be determined what mitigation measures might have played a role in reversing the rising trend of confirmed cases in this major outbreak. The government of Hong Kong has launched the mass rapid antigen tests (RAT) in the population and the StayHomeSafe scheme since February 2022. In this study, we examined the impact of the mass RAT on disease transmission and the case fatality ratio. It was suggested that the implementation of RAT plausibly played a role in the steady decrease of the effective reproduction number, leading to diminished SARS-CoV-2 transmission. In addition, we projected the disease burden of the outbreak in a scenario analysis to highlight the necessity of the StayHomeSafe scheme in Hong Kong. The Omicron outbreak experience in Hong Kong may provide actionable insights for navigating the challenges of COVID-19 surges in other regions and countries.

Infection rate and factors affecting close contacts of COVID-19 cases: A systematic review

OBJECTIVE

Contact tracing plays an essential role in mitigating the impact of an epidemic. During the COVID-19 pandemic, studies of those who have been in close contact with confirmed cases offer critical insights to understand the epidemiological characteristics of SARS-CoV-2 better. This study conducts a meta-analysis of existing studies' infection rates and affecting factors.

METHODS

We searched PubMed, Web of Science and CNKI from the inception to April 30 2022 to identify systematic reviews. Two reviewers independently extracted the data and assessed risk of bias. Meta-analyses were conducted to calculate pooled estimates by using Stata/SE 15.1 software.

RESULTS

There were 47 studies in the meta-analysis. Among COVID-19 close contacts, older age (RR = 1.94, 95% CI: 1.70, 2.21), contacts in households (RR = 2.83, 95% CI: 2.20, 3.65), and people in close contact with symptomatic infections (RR = 3.62, 95% CI: 1.88, 6.96) were associated with higher infection rates.

CONCLUSION

On average, each primary infection corresponded to 5.8 close contacts. Among COVID-19 close contacts, older age and contacts in households were associated with higher infection rates, and people in close contact with symptomatic infections had three times higher risk of infection compared to people in close contact with asymptomatic infections. In general, there are significantly more studies from China about close contacts, and the infection rate among close contacts was lower compared to other countries.

Impact of cross-border-associated cases on the SARS-CoV-2 epidemic in Switzerland during summer 2020 and 2021

During the summers of 2020 and 2021, the number of confirmed cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Switzerland remained at relatively low levels, but grew steadily over time. It remains unclear to what extent epidemic growth during these periods was a result of the relaxation of local control measures or increased traveling and subsequent importation of cases. A better understanding of the role of cross-border-associated cases (imports) on the local epidemic dynamics will help to inform future surveillance strategies. We analyzed routine surveillance data of confirmed cases of SARS-CoV-2 in Switzerland from 1 June to 30 September 2020 and 2021. We used a stochastic branching process model that accounts for superspreading of SARS-CoV-2 to simulate epidemic trajectories in absence and in presence of imports during summer 2020 and 2021. The Swiss Federal Office of Public Health reported 22,919 and 145,840 confirmed cases of SARS-CoV-2 from 1 June to 30 September 2020 and 2021, respectively. Among cases with known place of exposure, 27% (3,276 of 12,088) and 25% (1,110 of 4,368) reported an exposure abroad in 2020 and 2021, respectively. Without considering the impact of imported cases, the steady growth of confirmed cases during summer periods would be consistent with a value of R_e that is significantly above the critical threshold of 1. In contrast, we estimated R_e at 0.84 (95% credible interval, CrI: 0.78-0.90) in 2020 and 0.82 (95% CrI: 0.74-0.90) in 2021 when imported cases were taken into account, indicating that the local R_e was below the critical threshold of 1 during summer. In Switzerland, cross-border-associated SARS-CoV-2 cases had a considerable impact on the local transmission dynamics and can explain the steady growth of the epidemic during the summers of 2020 and 2021.

Coronavirus disease 2019 (COVID-19) symptoms, patient contacts, polymerase chain reaction (PCR) positivity and seropositivity among healthcare personnel in a Maryland healthcare system

In a large, system-wide, healthcare personnel (HCP) testing experience using severe acute respiratory coronavirus virus 2 (SARS-CoV-2) polymerase chain reaction (PCR) and serologic testing early in the coronavirus disease 2019 (COVID-19) pandemic, we did not find increased infection risk related to COVID-19 patient contact. Our findings support workplace policies for HCP protection and underscore the role of community exposure and asymptomatic infection.

Inferring selection effects in SARS-CoV-2 with Bayesian Viral Allele Selection

The global effort to sequence millions of SARS-CoV-2 genomes has provided an unprecedented view of viral evolution. Characterizing how selection acts on SARS-CoV-2 is critical to developing effective, long-lasting vaccines and other treatments, but the scale and complexity of genomic surveillance data make rigorous analysis challenging. To meet this challenge, we develop Bayesian Viral Allele Selection (BVAS), a principled and scalable probabilistic method for inferring the genetic determinants of differential viral fitness and the relative growth rates of viral lineages, including newly emergent lineages. After demonstrating the accuracy and efficacy of our method through simulation, we apply BVAS to 6.9 million SARS-CoV-2 genomes. We identify numerous mutations that increase fitness, including previously identified mutations in the SARS-CoV-2 Spike and Nucleocapsid proteins, as well as mutations in non-structural proteins whose contribution to fitness is less well characterized. In addition, we extend our baseline model to identify mutations whose fitness exhibits strong dependence on vaccination status as well as pairwise interaction effects, i.e. epistasis. Strikingly, both these analyses point to the pivotal role played by the N501 residue in the Spike protein. Our method, which couples Bayesian variable selection with a diffusion approximation in allele frequency space, lays a foundation for identifying fitness-associated mutations under the assumption that most alleles are neutral.

Association of symptom characteristics and comorbid conditions with viral RNA positivity of Covid-19 patients in Kasaragod district in Kerala, India: A retrospective cohort study

Background

Symptoms of Covid-19 are known to be non-specific ranging from asymptomatic cases to severe illness affecting multiple organ systems. The duration of viral RNA positivity and transmission varies in individuals. We describe the association between symptom characteristics and comorbid conditions with viral RNA positivity of SARSCoV-2 affected individuals.

Methods

We conducted a record-based retrospective cohort study of 179 patients found to be positive for Covid-19 in Kasaragod district in Kerala. We included details of all patients found positive during the initial phases of the pandemic and recorded details regarding symptoms, duration of viral RNA positivity and the occurrence of transmission. The data were analysed using SPSS.

Results

Any symptom was present in 68%. Fever (43%) was the most common symptom while 50% had at least one respiratory symptom. Increased duration of viral RNA positivity was found to be associated with presence of comorbid conditions. The majority of individuals who transmitted disease (75%) had some symptom, predominantly a respiratory symptom.

Conclusion

Respiratory symptoms are seen in half of the patients and viral RNA positivity was for a longer duration in patients with comorbid conditions.

Machine learning based regional epidemic transmission risks precaution in digital society

The contact and interaction of human is considered to be one of the important factors affecting the epidemic transmission, and it is critical to model the heterogeneity of individual activities in epidemiological risk assessment. In digital society, massive data makes it possible to implement this idea on large scale. Here, we use the mobile phone signaling to track the users' trajectories and construct contact network to describe the topology of daily contact between individuals dynamically. We show the spatiotemporal contact features of about 7.5 million mobile phone users during the outbreak of COVID-19 in Shanghai, China. Furthermore, the individual feature matrix extracted from contact network enables us to carry out the extreme event learning and predict the regional transmission risk, which can be further decomposed into the risk due to the inflow of people from epidemic hot zones and the risk due to people close contacts within the observing area. This method is much more flexible and adaptive, and can be taken as one of the epidemic precautions before the large-scale outbreak with high efficiency and low cost.

The impact of caregivers on nosocomial transmission during a COVID-19 outbreak in a community-based hospital in South Korea

The COVID-19 pandemic becomes a cause of concern for hospital transmission. Caregivers may play an important role as vectors for nosocomial infections; however, infection control for caregivers often is neglected. A nosocomial COVID-19 outbreak occurred in a 768-bed hospital from March 20, 2020, to April 14, 2020. We conducted a retrospective chart review and epidemiologic investigation on all cases. A total of 54 cases of laboratory-confirmed COVID-19 occurred in the community-based hospital. They included 26 (48.1%) patients, 21 (38.9%) caregivers, and 7 (13.0%) healthcare workers. These 21 caregivers cared for 18 patients, and of these, 9 were positive for COVID-19, 6 were negative, and 3 died before testing. Of the 6 negative patients, 3 had no exposure because the caregiver began to show symptoms at least 5 days after their discharge. Of the 9 positive patients, 4 cases of transmission took place from patient to caregiver (one patient transmitted COVID-19 to two caregivers), and 6 cases of transmission occurred from caregiver to patient. Of the 54 hospital-acquired cases, 38 occurred in the 8th-floor ward and 8 occurred in the 4th-floor ward. The index case of each ward was a caregiver. Counting the number of cases where transmission occurred only between patients and their own caregivers, 9 patients were suspected of having exposure to COVID-19 from their own caregivers. Six patients (66.7%) were infected by COVID-19-confirmed caregivers, and 3 patients were uninfected. Fewer patients among the infected were able to perform independent activities compared to uninfected patients. Not only patients and healthcare workers but also caregivers groups may be vulnerable to COVID-19 and be transmission sources of nosocomial outbreaks. Therefore, infection control programs for caregivers in addition to patients and healthcare workers can be equally important.

Can Hyperbaric Oxygen Therapy Be Used to Treat Children after COVID-19? A Bibliographic Review

The coronavirus disease (COVID-19) epidemic is a public health emergency of international concern. It was believed that SARS-CoV-2 virus was much less likely affect children. Statistics show that children account for 2-13% of all COVID-19 patients in individual countries. In the youngest population, acute respiratory failure is not as serious a problem as complications after COVID-19, mainly pediatric inflammatory multisystem syndrome (PIMS, MIS-C). This study used a bibliography review. The Medline database (using the PubMed platform) and the Cochrane Clinical Trials database were searched using the following keywords: hyperbaric oxygen therapy for children, treatment of children with COVID-19, and use of HBOT in the treatment of children following COVID-19. Thirteen publications that quantitatively and qualitatively described the efficacy of HBOT application in the treatment of pediatric diseases were eligible among the studies; those relating to the use of HBOT in the treatment of children with COVID-19 and its complications were not found. The bibliographic review showed that hyperbaric oxygen therapy can be used in the treatment of children after carbon monoxide poisoning, with soft tissue necrosis, bone necrosis, after burns, or after skin transplant. No evidence supported by research has been found in scientific journals on the effectiveness of the use of hyperbaric oxygen therapy in children with a history of COVID-19 infection. Research data are needed to develop evidence-driven strategies with regard to the use of HBOT therapy in the treatment of children and to reduce the number of pediatric patients suffering because of complications after COVID-19.

The COVID-19 Sentinel Schools Network of Catalonia (CSSNC) project: Associated factors to prevalence and incidence of SARS-CoV-2 infection in educational settings during the 2020-2021 academic year

The Sentinel Schools project was designed to monitor and evaluate the epidemiology of COVID-19 in Catalonia, gathering evidence for health and education policies to inform the development of health protocols and public health interventions to control of SARS-CoV-2 infection in schools. The aim of this study was to estimate the prevalence and incidence of SARS-CoV-2 infections and to identify their determinants among students and staff during February to June in the academic year 2020-2021. We performed two complementary studies, a cross-sectional and a longitudinal component, using a questionnaire to collect nominal data and testing for SARS-CoV-2 detection. We describe the results and perform a univariate and multivariate analysis. The initial crude seroprevalence was 14.8% (95% CI: 13.1-16.5) and 22% (95% CI: 18.3-25.8) for students and staff respectively, and the active infection prevalence was 0.7% (95% CI: 0.3-1) and 1.1% (95% CI: 0.1-2). The overall incidence for persons at risk was 2.73 per 100 person-month and 2.89 and 2.34 per 100 person-month for students and staff, respectively. Socioeconomic, self-reported knowledge, risk perceptions and contact pattern variables were positively associated with the outcome while sanitary measure compliance was negatively associated, the same significance trend was observed in multivariate analysis. In the longitudinal component, epidemiological close contact with SARS-CoV-2 infection was a risk factor for SARS-CoV-2 infection while the highest socioeconomic status level was protective as was compliance with sanitary measures. The small number of active cases detected in these schools suggests a low transmission among children in school and the efficacy of public health measures implemented, at least in the epidemiological scenario of the study period. The major contribution of this study was to provide results and evidence that help analyze the transmission dynamic of SARS-CoV-2 and evaluate the associations between sanitary protocols implemented, and measures to avoid SARS-CoV-2 spread in schools.

Outcomes of a Community Engagement and Information Gathering Program to Support Telephone-Based COVID-19 Contact Tracing: Descriptive Analysis

BACKGROUND

Contact tracing is an important public health tool for curbing the spread of infectious diseases. Effective and efficient contact tracing involves the rapid identification of individuals with infection and their exposed contacts and ensuring their isolation or quarantine, respectively. Manual contact tracing via telephone call and digital proximity app technology have been key strategies in mitigating the spread of COVID-19. However, many people are not reached for COVID-19 contact tracing due to missing telephone numbers or nonresponse to telephone calls. The New York City COVID-19 Trace program augmented the efforts of telephone-based contact tracers with information gatherers (IGs) to search and obtain telephone numbers or residential addresses, and community engagement specialists (CESs) made home visits to individuals that were not contacted via telephone calls.

OBJECTIVE

The aim of this study was to assess the contribution of information gathering and home visits to the yields of COVID-19 contact tracing in New York City.

METHODS

IGs looked for phone numbers or addresses when records were missing phone numbers to locate case-patients or contacts. CESs made home visits to case-patients and contacts with no phone numbers or those who were not reached by telephone-based tracers. Contact tracing management software was used to triage and queue assignments for the telephone-based tracers, IGs, and CESs. We measured the outcomes of contact tracing-related tasks performed by the IGs and CESs from July 2020 to June 2021.

RESULTS

Of 659,484 cases and 861,566 contact records in the Trace system, 28% (185,485) of cases and 35% (303,550) of contacts were referred to IGs. IGs obtained new phone numbers for 33% (61,804) of case-patients and 11% (31,951) of contacts; 50% (31,019) of the case-patients and 46% (14,604) of the contacts with new phone numbers completed interviews; 25% (167,815) of case-patients and 8% (72,437) of contacts were referred to CESs. CESs attempted 80% (132,781) of case and 69% (49,846) of contact investigations, of which 47% (62,733) and 50% (25,015) respectively, completed interviews. An additional 12,192 contacts were identified following IG investigations and 13,507 following CES interventions.

CONCLUSIONS

Gathering new or missing locating information and making home visits increased the number of case-patients and contacts interviewed for contact tracing and resulted in additional contacts. When possible, contact tracing programs should add information gathering and home visiting strategies to increase COVID-19 contact tracing coverage and yields as well as promote equity in the delivery of this public health intervention.

The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk

Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.

Clinical and Epidemiological Presentation of COVID-19 among Children in Conflict Setting

Background: This study aims to describe the observable symptoms of children with COVID-19 infection and analyze access to real-time polymerase chain reaction (RT-PCR) testing among children seeking care in Yemen. Method: In the period of March 2020−February 2022, data were obtained from 495 children suspected to have been infected with COVID-19 (from a larger register of 5634 patients) from the Diseases Surveillance and Infection Control Department at the Ministry of Public Health and Population in Aden, Yemen. Results: Overall, 21.4% of the children with confirmed COVID-19 infection were asymptomatic. Fever (71.4%) and cough (67.1%) were the most frequently reported symptoms among children, and children were less likely to have fever (p < 0.001), sore throat (p < 0.001) and cough (p < 0.001) compared to adults. A lower frequency of COVID-19-associated symptoms was reported among children with positive RT-PCR tests compared to children with negative tests. A lower rate of testing was conducted among children (25%) compared to adults (61%). Fewer tests were carried out among children <5 years (11%) compared to other age groups (p < 0.001), for children from other nationalities (4%) compared to Yemeni children (p < 0.001) and for girls (21%) compared to boys (30%) (p < 0.031). Conclusion: Understanding and addressing the cause of these disparities and improving guidelines for COVID-19 screening among children will improve access to care and control of the COVID-19 pandemic.

Use of temporal contact graphs to understand the evolution of COVID-19 through contact tracing data

Digital contact tracing has been recently advocated by China and many countries as part of digital prevention measures on COVID-19. Controversies have been raised about their effectiveness in practice as it remains open how they can be fully utilized to control COVID-19. In this article, we show that an abundance of information can be extracted from digital contact tracing for COVID-19 prevention and control. Specifically, we construct a temporal contact graph that quantifies the daily contacts between infectious and susceptible individuals by exploiting a large volume of location-related data contributed by 10,527,737 smartphone users in Wuhan, China. The temporal contact graph reveals five time-varying indicators can accurately capture actual contact trends at population level, demonstrating that travel restrictions (e.g., city lockdown) in Wuhan played an important role in containing COVID-19. We reveal a strong correlation between the contacts level and the epidemic size, and estimate several significant epidemiological parameters (e.g., serial interval). We also show that user participation rate exerts higher influence on situation evaluation than user upload rate does, indicating a sub-sampled dataset would be as good at prediction. At individual level, however, the temporal contact graph plays a limited role, since the behavior distinction between the infected and uninfected individuals are not substantial. The revealed results can tell the effectiveness of digital contact tracing against COVID-19, providing guidelines for governments to implement interventions using information technology.

The German COVID-19 Digital Contact Tracing App: A Socioeconomic Evaluation

The COVID-19 pandemic posed challenges to governments in terms of contact tracing. Like many other countries, Germany introduced a mobile-phone-based digital contact tracing solution ("Corona Warn App"; CWA) in June 2020. At the time of its release, however, it was hard to assess how effective such a solution would be, and a political and societal debate arose regarding its efficiency, also in light of its high costs. This study aimed to analyze the effectiveness of the CWA, considering prevented infections, hospitalizations, intensive care treatments, and deaths. In addition, its efficiency was to be assessed from a monetary point of view, and factors with a significant influence on the effectiveness and efficiency of the CWA were to be determined. Mathematical and statistical modeling was used to calculate infection cases prevented by the CWA, along with the numbers of prevented complications (hospitalizations, intensive care treatments, deaths) using publicly available CWA download numbers and incidences over time. The monetized benefits of these prevented cases were quantified and offset against the costs incurred. Sensitivity analysis was used to identify factors critically influencing these parameters. Between June 2020 and April 2022, the CWA prevented 1.41 million infections, 17,200 hospitalizations, 4600 intensive care treatments, and 7200 deaths. After offsetting costs and benefits, the CWA had a net present value of EUR 765 m in April 2022. Both the effectiveness and efficiency of the CWA are decisively and disproportionately positively influenced by the highest possible adoption rate among the population and a high rate of positive infection test results shared via the CWA.

Trends in SARS-CoV-2 infection prevalence during England's roadmap out of lockdown, January to July 2021

BACKGROUND

Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.

AIM

We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence.

METHODS

On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions.

RESULTS

Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups.

CONCLUSION

High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays/closures playing a significant part.

Promoting Compliance to COVID-19 Vaccination in Military Units

BACKGROUND

On December 27th, 2020, the Israeli Defense Forces initiated a mass COVID-19 vaccination campaign aiming to vaccinate its personnel. This population upheld specific characteristics in terms of age and sex, lack of significant comorbidities, and a general scarcity of risk factors for sustaining a severe COVID-19 illness. We present the measures taken to increase vaccination compliance, and the vaccination rate that followed these actions. Our secondary goal was to compare between vaccination rates in frontline battalions and highly essential military units (group A) and rear administration and support military units (group B).

METHODS

This was a retrospective review that included 70 military units that were composed of 18,719 individuals of both sexes, mostly free of significant comorbidities. We divided the challenges of maximizing vaccination rates into two main categories: vaccine compliance (including communication and information) and logistical challenges. We compared the vaccination rates in groups A and B using a multivariable linear regression model. A P-value of .05 was considered significant.

RESULTS

The mean age in 70 military units was 22.77 ± 1.35 (range 18-50) years, 71.13% males. A total of 726 (3.88%) individuals have been found positive for SARS-CoV-2 between March 1st, 2020 and February 18th, 2021. On February 18th, 2021, 54 days after the vaccination campaign was launched, 15,871 (84.79%) of the study population have been vaccinated by the first dose of Pfizer COVID-19 vaccine, expressing an 88.21% compliance rate (excluding recovered COVID-19 cases who were not prioritized to be vaccinated at this stage). Vaccination compliance in military units from group A was found to be higher when compared to group B (P < .001), leading to a 90.02% of group A population being either previously SARS-CoV-2 positive or COVID-19 vaccinated.

CONCLUSIONS

A designated army campaign led by a multidisciplinary team could rapidly achieve a high COVID-19 vaccination rate. The information presented can serve organizations worldwide with similar characteristics that plan a mass COVID-19 vaccination campaign.

Close Contacts, Infected Cases, and the Trends of SARS-CoV-2 Omicron Epidemic in Shenzhen, China

(1) The overall trends of the number of daily close contacts and infected cases as well as their association during an epidemic of Omicron Variant of SARS-CoV-2 have been poorly described. (2) Methods: This study was to describe the trends during the epidemic of the Omicron variant of SARS-CoV-2 in Shenzhen, China, including the number of close contacts and infected cases as well as their ratios by days and stages (five stages). (3) Results: A total of 1128 infected cases and 80,288 close contacts were identified in Shenzhen from 13 February 2022 to 1 April 2022. Before the citywide lockdown (14 March), the number of daily close contacts and infected cases gradually increased. However, the numbers showed a decrease after the lockdown was imposed. The ratio of daily close contacts to daily infected cases ranged from 20.2:1 to 63.4:1 and reached the lowest during the lockdown period. The growth rate of daily close contacts was consistent with those of infected cases observed 6 days later to some extent. (4) Conclusions: The Omicron variant epidemic was promptly contained by tracing close contacts and taking subsequent quarantine measures.

Contact tracing reveals community transmission of COVID-19 in New York City

Understanding SARS-CoV-2 transmission within and among communities is critical for tailoring public health policies to local context. However, analysis of community transmission is challenging due to a lack of high-resolution surveillance and testing data. Here, using contact tracing records for 644,029 cases and their contacts in New York City during the second pandemic wave, we provide a detailed characterization of the operational performance of contact tracing and reconstruct exposure and transmission networks at individual and ZIP code scales. We find considerable heterogeneity in reported close contacts and secondary infections and evidence of extensive transmission across ZIP code areas. Our analysis reveals the spatial pattern of SARS-CoV-2 spread and communities that are tightly interconnected by exposure and transmission. We find that locations with higher vaccination coverage and lower numbers of visitors to points-of-interest had reduced within- and cross-ZIP code transmission events, highlighting potential measures for curtailing SARS-CoV-2 spread in urban settings.