PCT-TEE: Trajectory-based Private Contact Tracing System with Trusted Execution Environment

Existing Bluetooth-based private contact tracing (PCT) systems can privately detect whether people have come into direct contact with patients with COVID-19. However, we find that the existing systems lack functionality and flexibility , which may hurt the success of contact tracing. Specifically, they cannot detect indirect contact (e.g., people may be exposed to COVID-19 by using a contaminated sheet at a restaurant without making direct contact with the infected individual); they also cannot flexibly change the rules of “risky contact,” such as the duration of exposure or the distance (both spatially and temporally) from a patient with COVID-19 that is considered to result in a risk of exposure, which may vary with the environmental situation. In this article, we propose an efficient and secure contact tracing system that enables us to trace both direct contact and indirect contact. To address the above problems, we need to utilize users’ trajectory data for PCT, which we call trajectory-based PCT . We formalize this problem as a spatiotemporal private set intersection that satisfies both the security and efficiency requirements. By analyzing different approaches such as homomorphic encryption, which could be extended to solve this problem, we identify the trusted execution environment (TEE) as a candidate method to achieve our requirements. The major challenge is how to design algorithms for a spatiotemporal private set intersection under the limited secure memory of the TEE. To this end, we design a TEE-based system with flexible trajectory data encoding algorithms. Our experiments on real-world data show that the proposed system can process hundreds of queries on tens of millions of records of trajectory data within a few seconds.

A novel predictive model for capturing threats for facilitating effective social distancing in COVID-19

Social distancing is one of the simple and effective shields for every individual to control spreading of virus in present scenario of pandemic coronavirus disease (COVID-19). However, existing application of social distancing is a basic model and it is also characterized by various pitfalls in case of dynamic monitoring of infected individual accurately. Review of existing literature shows that there has been various dedicated research attempt towards social distancing using available technologies, however, there are further scope of improvement too. This paper has introduced a novel framework which is capable of computing the level of threat with much higher degree of accuracy using distance and duration of stay as elementary parameters. Finally, the model can successfully classify the level of threats using deep learning. The study outcome shows that proposed system offers better predictive performance in contrast to other approaches.

Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant

Background. The Omicron SARS-CoV-2 variant is responsible for a major wave of COVID-19, with record case counts reflecting high transmissibility and escape from prior immunity. Defining the time course of Omicron viral proliferation and clearance is crucial to inform isolation protocols aiming to minimize disease spread. Methods. We obtained longitudinal, quantitative RT-qPCR test results using combined anterior nares and oropharyngeal samples (n = 10,324) collected between July 5th, 2021 and January 10th, 2022 from the National Basketball Association's (NBA) occupational health program. We quantified the fraction of tests with PCR cycle threshold (Ct) values <30, chosen as a proxy for potential infectivity and antigen test positivity, on each day after first detection of suspected and confirmed Omicron infections, stratified by individuals detected under frequent testing protocols and those detected due to symptom onset or concern for contact with an infected individual. We quantified the duration of viral proliferation, clearance rate, and peak viral concentration for individuals with acute Omicron and Delta variant SARS-CoV-2 infections. Results. A total of 97 infections were confirmed or suspected to be from the Omicron variant and 107 from the Delta variant. Of 27 Omicron-infected individuals testing positive ≤1 day after a previous negative or inconclusive test, 52.0% (13/25) were PCR positive with Ct values <30 at day 5, 25.0% (6/24) at day 6, and 13.0% (3/23) on day 7 post detection. Of 70 Omicron-infected individuals detected ≥2 days after a previous negative or inconclusive test, 39.1% (25/64) were PCR positive with Ct values <30 at day 5, 33.3% (21/63) at day 6, and 22.2% (14/63) on day 7 post detection. Overall, Omicron infections featured a mean duration of 9.87 days (95% CI 8.83-10.9) relative to 10.9 days (95% CI 9.41-12.4) for Delta infections. The peak viral RNA based on Ct values was lower for Omicron infections than for Delta infections (Ct 23.3, 95% CI 22.4-24.3 for Omicron; Ct 20.5, 95% CI 19.2-21.8 for Delta) and the clearance phase was shorter for Omicron infections (5.35 days, 95% CI 4.78-6.00 for Omicron; 6.23 days, 95% CI 5.43-7.17 for Delta), though the rate of clearance was similar (3.13 Ct/day, 95% CI 2.75-3.54 for Omicron; 3.15 Ct/day, 95% CI 2.69-3.64 for Delta). Conclusions. While Omicron infections feature lower peak viral RNA and a shorter clearance phase than Delta infections on average, it is unclear to what extent these differences are attributable to more immunity in this largely vaccinated population or intrinsic characteristics of the Omicron variant. Further, these results suggest that Omicron's infectiousness may not be explained by higher viral load measured in the nose and mouth by RT-PCR. The substantial fraction of individuals with Ct values <30 at days 5 of infection, particularly in those detected due to symptom onset or concern for contact with an infected individual, underscores the heterogeneity of the infectious period, with implications for isolation policies.

Dynamics and optimal control of a spatial diffusion HIV/AIDS model with ART and PrEP treatments

In this paper, to investigate the synthetic effect of PrEP (pre-exposure prophylaxis) and ART (antiretrovial therapy) on HIV transmission among MSM (men who have sex with men) in heterogenous environment, an realistic HIV epidemic model with spatial diffusion is established. Here, HIV infectious people are divided into three immunity based compartments, i.e., CD4+ T cell count less than 350, between 350 and 500, and more than 500, respectively. The basic reproduction number $R_0$ is established and proved as a threshold parameter: The global asymptotic stability of the disease-free steady state holds for $R_0<1$, and the disease will be present if $R_0>1$. Considering the substantial advantages of PrEP and ART in controlling HIV transmissions among MSM, the optimal control problem is presented for the case of positive constant diffusion coefficients, which minimize the total population of susceptible individual and HIV infected individual, the cost of PrEP and ART thearpy. As an illustration of our theoretical results, we conduct numerical simulations. We also conduct an optimal control case study where model parameters are estimated from the demographic and epidemiological data from China. This work suggests: (1) Spatial factors cannot be ignored during the HIV intervention; (2)Taking the PrEP intervention measure for HIV transmissions among MSM as early as possible will help to improve the control efficiency and reduces its cost; (3) Reducing the PrEP drug costs will promote the efficiency of PrEP treatment in preventing the spread of HIV among MSM.

SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection

In-depth analysis of SARS-CoV-2 quasispecies is pivotal for a thorough understating of its evolution during infection. The recent deployment of COVID-19 vaccines, which elicit protective anti-spike neutralizing antibodies, has stressed the importance of uncovering and characterizing SARS-CoV-2 variants with mutated spike proteins. Sequencing databases have allowed to follow the spread of SARS-CoV-2 variants that are circulating in the human population, and several experimental platforms were developed to study these variants. However, less is known about the SARS-CoV-2 variants that are developed in the respiratory system of the infected individual. To gain further insight on SARS-CoV-2 mutagenesis during natural infection, we preformed single-genome sequencing of SARS-CoV-2 isolated from nose-throat swabs of infected individuals. Interestingly, intra-host SARS-CoV-2 variants with mutated S genes or N genes were detected in all individuals who were analyzed. These intra-host variants were present in low frequencies in the swab samples and were rarely documented in current sequencing databases. Further examination of representative spike variants identified by our analysis showed that these variants have impaired infectivity capacity and that the mutated variants showed varied sensitivity to neutralization by convalescent plasma and to plasma from vaccinated individuals. Notably, analysis of the plasma neutralization activity against these variants showed that the L1197I mutation at the S2 subunit of the spike can affect the plasma neutralization activity. Together, these results suggest that SARS-CoV-2 intra-host variants should be further analyzed for a more thorough characterization of potential circulating variants.

Comparison of an Air-Fed Mask System with Hospital-Issued Personal Protection Equipments for Dental Aerosol Protection During the COVID-19 Pandemic

Aim: A pilot study was conducted with the aim of developing a system to protect the eyes, nose, and mouth from the aerosol generated from a high-speed dental handpiece during the COVID-19 pandemic. Background: The SARS-CoV-2 virus is known to be present in the saliva of an infected individual during the contagious viral shedding phase of the disease. The use of rotary dental instruments places oral health practitioners at risk of contracting COVID-19 from infected individuals. In particular, it is very difficult to protect the mucous membranes of the face against the extremely fine aerosol produced from a high-speed dental handpiece. Objectives: This study aimed to develop and test a novel PPE system for use during the COVID-19 pandemic. An air-fed spray-painting mask was used under a plastic hood to protect against the aerosol from a high-speed dental handpiece. This was found to be superior compared to hospital-issued N-95 masks and eye protection in our test model. Methods: Subjects donned various forms of PPE whilst using a high-speed dental handpiece in a confined cubicle. The efficacy of each form of PPE was evaluated by adding fluorescein to the water coolant supply line of a high-speed dental handpiece before checking for facial contamination with an ophthalmology slit lamp. Results: Under our test conditions, the N-95 mask did not prevent nasal and mouth contaminations, but the combination of an air-fed mask with a sealed hood prevented these contaminations. Although goggles worn tightly did prevent contamination, the air-fed mask system was far more comfortable and did not fog up. Discussion: Under the rigorous test conditions of our model, we found hospital-issued PPE ineffective. We also found the single strategy of using positive airflow into a face mask ineffective, even with extremely high levels of airflow. Complete protection was only achieved reliably by the combination of physically sealing off the face from the surrounding airspace and using the air-fed system to provide an external source of air to breathe. We effectively made the clinical equivalent of a dive bell helmet. The air-fed mask is supplied by a standard dental air compressor and is simple to install for someone familiar with the technical aspects of compressors. The compressor does not rely on a filter and proves effective with cheap and easily accessible disposable items. Conclusion: Under rigorous testing conditions, the developed air-fed mask system with a sealed hood on low flow performed better than hospital-issued PPE against high-speed dental aerosol protection. The developed system protects the operators from the air of the room contaminated with aerosol and brings in safe air from the outside for them to breathe.

Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework

Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, Rt, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and Rt. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of Rt are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and Rt that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.

Is the increased transmissibility of SARS-CoV-2 variants driven by within or outside-host processes?

Understanding the factors that increase the transmissibility of the recently emerging variants of SARS-CoV-2 can aid in mitigating the COVID-19 pandemic. The enhanced transmissibility could be attributed to enhanced within-host processes, such as contagiousness (viral shedding by an infected individual) and infectivity (the probability of a susceptible individual to get infected), or outside-host processes, such as viral stability on surfaces and in the air. We utilized a mathematical model in order to theoretically analyze the specific mechanisms of virus transfer between an infected and susceptible individual. This allowed us to examine how the within-host or outside-host processes affect the overall viral transmission. Our analysis is based the available data on the Alpha, Epsilon and Delta variants as well as the currently emerging Omicron variant. We found that the higher transmissibility of the SARS-CoV-2 variants can be attributed only to within-host processes. Specifically, enhanced contagiousness drives the Delta variant transmissibility, while the Alpha, Epsilon and Omicron are characterized by an enhanced infectivity. Since outside-host processes have little contribution to the observed increase in the transmissibility, leading stricter hygienic and behavioral measures than those that were already applied are not expected to achieve a pronounced mitigating effect.

Staphylococcus aureus in poultry, with special emphasis on methicillin-resistant strain infection: A comprehensive review from one health perspective

Staphylococcus aureus is a Gram-positive coccus normally present on the skin and internal organs of animals, birds, and humans. Under certain conditions, S. aureus could produce septicemia and affection of the skin, joints, and heart, as well as sepsis and death. The pathogenicity of S. aureus is associated with the presence of some virulent surface proteins and the production of some virulent toxins and enzymes. This pathogen is considered one of the most important and worldwide foodborne causes as it is incriminated in most cases of food poisoning. The hazardous use of antibiotics in the veterinary field leads to the development of multidrug-resistant S. aureus strains that can be transmitted to humans. The incidence of methicillin-resistant S. aureus (MRSA) strains has increased globally. These resistant strains have been detected in live animals, poultry, and humans. In addition, retail animal products, especially those of avian origin, are considered the main source of MRSA strains that can be easily transmitted to humans. MRSA infection is regarded as nosocomial or occupational. Humans get infected with MRSA strains through improper handling or preparation of contaminated animals or poultry carcasses or improper cooking with contaminated meat. Live birds also can transmit MRSA to close-contact workers in poultry farms. Transmission of MRSA infection in hospitals is from an infected individual to a healthy one. Prevention and control of MRSA are based on the application of hygienic measures in farms as well as proper processing, handling, and cooking of retail poultry products. The cooperation between veterinary and human practitioners is a must to avoid the possibility of zoonotic transmission. Accordingly, this review focused on the sources and transmission of MRSA infection, virulence and resistance factors, incidence and prevalence in poultry and different products, antibiotic resistance, and prevention and control strategies.

Reducing Virus Transmission from Heating, Ventilation, and Air Conditioning Systems of Urban Subways

Transmission via virus-carrying aerosols inside enclosed spaces is an important transmission mode for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as supported by growing evidence. The urban subway is one of the most commonly used enclosed spaces. The subway is a utilitarian and low-cost transit system in today’s society. However, studies are yet to demonstrate patterns of viral transmission in subway heating, ventilation, and air conditioning (HVAC) systems. To fill this gap, we performed a computational investigation of the airflow (and the associated aerosol transmission) in an urban subway cabin equipped with an HVAC system. We employed a transport equation for aerosol concentration, which was added to the basic buoyant solver to resolve aerosol transmission inside the subway cabin. This was achieved by considering the thermal, turbulence, and induced ventilation flow effects. Using the aerosol encounter probability over sampling lines crossing the passenger breathing zones, we can detect the highest infection risk zones inside the urban subway under different settings. We proposed a novel HVAC system that can impede aerosol spread, both vertically and horizontally, inside the cabin. In the conventional model, the maximum aerosol encounter probability from an infected individual breathing near the fresh-air ducts was equal to 15%. This decreased to 0.36% in the proposed HVAC model. Overall, using the proposed HVAC system for urban subways decreased the mean value of the aerosol encounter probability by approximately 79% compared to that for the conventional system.