Increased close proximity airborne transmission of the SARS-CoV-2 Delta variant

SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia

The severe acute respiratory syndrome coronavirus 2 pandemic is characterized by the emergence of novel variants of concern (VOCs) that replace ancestral strains. Here, we dissect the complex selective pressures by evaluating variant fitness and adaptation in human respiratory tissues. We evaluate viral properties and host responses to reconstruct forces behind D614G through Omicron (BA.1) emergence. We observe differential replication in airway epithelia, differences in cellular tropism, and virus-induced cytotoxicity. D614G accumulates the most mutations after infection, supporting zoonosis and adaptation to the human airway. We perform head-to-head competitions and observe the highest fitness for Gamma and Delta. Under these conditions, RNA recombination favors variants encoding the B.1.617.1 lineage 3' end. Based on viral growth kinetics, Alpha, Gamma, and Delta exhibit increased fitness compared to D614G. In contrast, the global success of Omicron likely derives from increased transmission and antigenic variation. Our data provide molecular evidence to support epidemiological observations of VOC emergence.

Omicron and Delta variant prevalence detection and identification during the fourth COVID-19 wave in Mexico using wastewater-based epidemiology

Objectives

To identify the SARS-CoV-2 variants Delta and Omicron during the fourth wave of the COVID-19 pandemic in Mexico using samples taken from 19 locations in 18 out of the 32 states.

Methods

The genetic material concentration was done with PEG/NaCl precipitation, SARS-CoV-2 presence was confirmed by reverse transcriptase-quantitative polymerase chain reaction assay, the variant detection was carried out using a commercial mutation detection panel kit, and variant/mutation confirmation was done by amplicon sequencing of receptor-binding domain target region. The study used 41 samples.

Results

The Delta variant was confirmed in two samples during August 2021 (Querétaro and CDMX) and in three samples during November 2021 (Aguascalientes, Ciudad Juárez campuses, and Nuevo Leon). In December 2021, another sample with the Delta variant was confirmed in Nuevo Leon. Between January to March 2022 only the presence of Omicron was confirmed, (variant BA.1). Additionally, in this period six samples were identified with the status "Variant Not Determined".

Conclusion

To our knowledge, this study is one of the first to identify Omicron and Delta variants with polymerase chain reaction in Mexico and Latin America and its distribution across the country with 56% Mexican states making it a viable alternative for variant detection without conducting a large quantity of sequencing of clinical tests.

Access to health and social protection policies by homeless people during the COVID-19 pandemic: a mixed-methods case study on tailored inter-sector care during a health emergency

Introduction

The article analyzed homeless people's (HP) access to health and social protection policies and tailored inter-sector care, including emergency measures, during the COVID-19 pandemic in Belo Horizonte (BH), capital of Minas Gerais state, Brazil. It intended to provide data on HP and evaluate existing public policies focused on vulnerable populations during this health emergency.

Methods

The study adopted a mixed-methods design with triangulation of quantitative and qualitative data.

Results

Social cartography showed that in the early months of the pandemic, the health administration had difficulty reordering the health system, which experienced constant updates in the protocols but was nevertheless consolidated over the months. The evidence collected in the study showed that important emergency interventions in the municipality of BH involved activities that facilitated access by HP to the supply of services.

Discussion

The existence of national guidelines for inter-sector care for HP cannot be ruled out as a positive influence, although the municipalities are responsible for their implementation. Significantly, a health emergency was necessary to intensify the relationship between health and social protection services. Roving services were among those with the greatest positive evidence, with the least need for infrastructure to be replicated at the local level. In addition, the temporary supply of various inter-sector services, simultaneously with the provision of day shelters by organized civil society, was considered a key factor for expanding and intensifying networks of care for HP during the emergency phase. A plan exists to continue and expand this model in the future. The study concluded that understanding the inter-sector variables that impact HP contributes to better targeting of investments in interventions that work at the root causes of these issues or that increase the effectiveness of health and social protection systems.

Airborne transmission risks of tuberculosis and COVID-19 in schools in South Africa, Switzerland, and Tanzania: Modeling of environmental data

The COVID-19 pandemic renewed interest in airborne transmission of respiratory infections, particularly in congregate indoor settings, such as schools. We modeled transmission risks of tuberculosis (caused by Mycobacterium tuberculosis, Mtb) and COVID-19 (caused by SARS-CoV-2) in South African, Swiss and Tanzanian secondary schools. We estimated the risks of infection with the Wells-Riley equation, expressed as the median with 2.5% and 97.5% quantiles (credible interval [CrI]), based on the ventilation rate and the duration of exposure to infectious doses (so-called quanta). We computed the air change rate (ventilation) using carbon dioxide (CO2) as a tracer gas and modeled the quanta generation rate based on reported estimates from the literature. The share of infectious students in the classroom is determined by country-specific estimates of pulmonary TB. For SARS-CoV-2, the number of infectious students was estimated based on excess mortality to mitigate the bias from country-specific reporting and testing. Average CO2 concentration (parts per million [ppm]) was 1,610 ppm in South Africa, 1,757 ppm in Switzerland, and 648 ppm in Tanzania. The annual risk of infection for Mtb was 22.1% (interquartile range [IQR] 2.7%-89.5%) in South Africa, 0.7% (IQR 0.1%-6.4%) in Switzerland, and 0.5% (IQR 0.0%-3.9%) in Tanzania. For SARS-CoV-2, the monthly risk of infection was 6.8% (IQR 0.8%-43.8%) in South Africa, 1.2% (IQR 0.1%-8.8%) in Switzerland, and 0.9% (IQR 0.1%-6.6%) in Tanzania. The differences in transmission risks primarily reflect a higher incidence of SARS-CoV-2 and particularly prevalence of TB in South Africa, but also higher air change rates due to better natural ventilation of the classrooms in Tanzania. Global comparisons of the modeled risk of infectious disease transmission in classrooms can provide high-level information for policy-making regarding appropriate infection control strategies.

Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan

Japan has implemented a cluster-based approach for coronavirus disease 2019 (COVID-19) from the pandemic's beginning based on the transmission heterogeneity (overdispersion) of severe acute respiratory coronavirus 2 (SARS-CoV-2). However, studies analyzing overdispersion of transmission among new variants of concerns (VOCs), especially for Omicron, were limited. Thus, we aimed to clarify how the transmission heterogeneity has changed with the emergence of VOCs (Alpha, Delta, and Omicron) using detailed contact tracing data in Yamagata Prefecture, Japan. We estimated the time-varying dispersion parameter ([Formula: see text]) by fitting a negative binomial distribution for each transmission generation. Our results showed that even after the emergence of VOCs, there was transmission heterogeneity of SARS-CoV-2, with changes in [Formula: see text] during each wave. Continuous monitoring of transmission dynamics is vital for implementing appropriate measures. However, a feasible and sustainable epidemiological analysis system should be established to make this possible.

Monitoring of COVID-19 in wastewater across the Eastern Upper Peninsula of Michigan

Wastewater-based epidemiology is being used as a tool to monitor the spread of COVID-19 and provide an early warning for the presence or increase of clinical cases in a community. The majority of wastewater-based epidemiology for COVID-19 tracking has been utilized in sewersheds that service populations in the tens-to-hundreds of thousands. Few studies have been conducted to assess the usefulness of wastewater in predicting COVID-19 clinical cases specifically in rural areas. This study collected samples from 16 locations across the Eastern Upper Peninsula of Michigan from June to December 2021. Sampling locations included 12 rural municipalities, a Tribal housing community and casino, a public university, three municipalities that also contained a prison, and a small island with heavy tourist traffic. Samples were analyzed for SARS-CoV-2 N1, N2, and variant gene copies using reverse transcriptase droplet digital polymerase chain reaction (RT-ddPCR). Wastewater N1 and N2 gene copies and clinical case counts were correlated to determine if wastewater results were predictive of clinical cases. Significant correlation between N1 and N2 gene copies and clinical cases was found for all sites (⍴= 0.89 to 0.48). N1 and N2 wastewater results were predictive of clinical case trends within 0-7 days. The Delta variant was detected in the Pickford and St. Ignace samples more than 12-days prior to the first reported Delta clinical cases in their respective counties. Locations with low correlation could be attributed to their high rates of tourism. This is further supported by the high correlation seen in the public university, which is a closed population. Long-term wastewater monitoring over a large, rural geographic area is useful for informing the public of potential outbreaks in the community regardless of asymptomatic cases and access to clinical testing.

Respiratory aerosol particle emission and simulated infection risk is greater during indoor endurance than resistance exercise

Pathogens such as severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), influenza, and rhinoviruses are transmitted by airborne aerosol respiratory particles that are exhaled by infectious subjects. We have previously reported that the emission of aerosol particles increases on average 132-fold from rest to maximal endurance exercise. The aims of this study are to first measure aerosol particle emission during an isokinetic resistance exercise at 80% of the maximal voluntary contraction until exhaustion, second to compare aerosol particle emission during a typical spinning class session versus a three-set resistance training session. Finally, we then used this data to calculate the risk of infection during endurance and resistance exercise sessions with different mitigation strategies. During a set of isokinetic resistance exercise, aerosol particle emission increased 10-fold from 5,400 ± 1,200 particles/min at rest to 59,000 ± 69,900 particles/min during a set of resistance exercise. We found that aerosol particle emission per minute is on average 4.9-times lower during a resistance training session than during a spinning class. Using this data, we determined that the simulated infection risk increase during an endurance exercise session was sixfold higher than during a resistance exercise session when assuming one infected participant in the class. Collectively, this data helps to select mitigation measures for indoor resistance and endurance exercise classes at times where the risk of aerosol-transmitted infectious disease with severe outcomes is high.

Effect of indoor temperature on the velocity fields and airborne transmission of sneeze droplets: An experimental study and transient CFD modeling

The spread of the COVID-19 pandemic through the airborne transmission of coronavirus-containing droplets emitted during coughing, sneezing, and speaking has now been well recognized. This study presented the effect of indoor temperature (T∞) on the airflow dynamics, velocity fields, size distribution, and airborne transmission of sneeze droplets in a confined space through experimental investigation and computational fluid dynamic (CFD) modeling. The CFD simulations were performed using the renormalization group k-ε turbulence model. The experimental shadowgraph imaging and CFD simulations showed the time evolution of sneeze droplet concentrations into the turbulent expanded puff, droplet cloud, and fully-dispersed droplets. Also, the predicted mean velocity of droplets was compared with the obtained experimental data to assess the accuracy of the results. In addition, the validated computational model was used to study the sneeze complex airflow behavior and airborne transmission of small, medium, and large respiratory droplets in confined spaces at different temperatures. The warm room showed more than ∼14 % increase in airborne aerosols than the room with a mild temperature. The study provides information on the effect of room temperature on the evaporation of respiratory droplets during sneezing. The findings of this fundamental study may be used in developing exposure guidelines by controlling the temperature level in indoor environments to reduce the exposure risk of COVID-19.

Increasing ventilation reduces SARS-CoV-2 airborne transmission in schools: A retrospective cohort study in Italy's Marche region

Introduction

While increasing the ventilation rate is an important measure to remove inhalable virus-laden respiratory particles and lower the risk of infection, direct validation in schools with population-based studies is far from definitive.

Methods

We investigated the strength of association between ventilation and SARS-CoV-2 transmission reported among the students of Italy's Marche region in more than 10,000 classrooms, of which 316 were equipped with mechanical ventilation. We used ordinary and logistic regression models to explore the relative risk associated with the exposure of students in classrooms.

Results and discussion

For classrooms equipped with mechanical ventilation systems, the relative risk of infection of students decreased at least by 74% compared with a classroom with only natural ventilation, reaching values of at least 80% for ventilation rates >10 L s-1 student-1. From the regression analysis we obtained a relative risk reduction in the range 12%15% for each additional unit of ventilation rate per person. The results also allowed to validate a recently developed predictive theoretical approach able to estimate the SARS-CoV-2 risk of infection of susceptible individuals via the airborne transmission route. We need mechanical ventilation systems to protect students in classrooms from airborne transmission; the protection is greater if ventilation rates higher than the rate needed to ensure indoor air quality (>10 L s-1 student-1) are adopted. The excellent agreement between the results from the retrospective cohort study and the outcome of the predictive theoretical approach makes it possible to assess the risk of airborne transmission for any indoor environment.

A comprehensive modelling approach to estimate the transmissibility of coronavirus and its variants from infected subjects in indoor environments

A central issue in assessing the airborne risk of COVID-19 infections in indoor spaces pertains to linking the viral load in infected subjects to the lung deposition probability in exposed individuals through comprehensive aerosol dynamics modelling. In this paper, we achieve this by combining aerosol processes (evaporation, dispersion, settling, lung deposition) with a novel double Poisson model to estimate the probability that at least one carrier particle containing at least one virion will be deposited in the lungs and infect a susceptible individual. Multiple emission scenarios are considered. Unlike the hitherto used single Poisson models, the double Poisson model accounts for fluctuations in the number of carrier particles deposited in the lung in addition to the fluctuations in the virion number per carrier particle. The model demonstrates that the risk of infection for 10-min indoor exposure increases from 1 to 50% as the viral load in the droplets ejected from the infected subject increases from 2 × 108 to 2 × 1010 RNA copies/mL. Being based on well-established aerosol science and statistical principles, the present approach puts airborne risk assessment methodology on a sound formalistic footing, thereby reducing avoidable epistemic uncertainties in estimating relative transmissibilities of different coronavirus variants quantified by different viral loads.

Lockdowns exert selection pressure on overdispersion of SARS-CoV-2 variants

The SARS-CoV-2 ancestral strain has caused pronounced superspreading events, reflecting a disease characterized by overdispersion, where about 10% of infected people cause 80% of infections. New variants of the disease have different person-to-person variability in viral load, suggesting for example that the Alpha (B.1.1.7) variant is more infectious but relatively less prone to superspreading. Meanwhile, non-pharmaceutical mitigation of the pandemic has focused on limiting social contacts (lockdowns, regulations on gatherings) and decreasing transmission risk through mask wearing and social distancing. Using a mathematical model, we show that the competitive advantage of disease variants may heavily depend on the restrictions imposed. In particular, we find that lockdowns exert an evolutionary pressure which favours variants with lower levels of overdispersion. Our results suggest that overdispersion is an evolutionarily unstable trait, with a tendency for more homogeneously spreading variants to eventually dominate.

•

Novel variants of SARS-CoV-2 appear to be less prone to superspreading.

•

A new model shows that it is advantageous for the pathogen to spread homogeneously.

•

Interventions exert a selective pressure towards developing homogeneous transmission.

•

The results have implications for the assessment of novel variants.

•

Adds to understanding of how behaviour and interventions shape pathogen evolution.

A Potent Neutralizing Nanobody Targeting the Spike Receptor-Binding Domain of SARS-CoV-2 and the Structural Basis of Its Intimate Binding

The continuous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) around the world has raised unprecedented challenges to the human society. Antibodies and nanobodies possessing neutralization activity represent promising drug candidates. In this study, we report the identification and characterization of a potent SARS-CoV-2 neutralizing nanobody that targets the viral spike receptor-binding domain (S-RBD). The nanobody, termed as Nb-007, engages SARS-CoV-2 S-RBD with the two-digit picomolar binding affinity and shows outstanding virus entry-inhibition activity. The complex structure of Nb-007 bound to SARS-CoV-2 S-RBD reveals an epitope that is partially overlapping with the binding site for the human receptor of angiotensin-converting enzyme 2 (ACE2). The nanobody therefore exerts neutralization by competing with ACE2 for S-RBD binding, which is further ascertained by our in-vitro biochemical analyses. Finally, we also show that Nb-007 reserves promising, though compromised, neutralization activity against the currently-circulating Delta variant and that fusion of the nanobody with Fc dramatically increases its entry-inhibition capacity. Taken together, these data have paved the way of developing Nb-007 as a drug-reserve for potential treatment of SARS-CoV-2 related diseases.

Numerical Flow Simulation on the Virus Spread of SARS-CoV-2 Due to Airborne Transmission in a Classroom

In order to continue using highly frequented rooms such as classrooms, seminar rooms, offices, etc., any SARS-CoV-2 virus concentration that may be present must be kept low or reduced through suitable ventilation measures. In this work, computational fluid dynamics (CFD) is used to develop a virtual simulation model for calculating and analysing the viral load due to airborne transmission in indoor environments aiming to provide a temporally and spatially-resolved risk assessment with explicit relation to the infectivity of SARS-CoV-2. In this work, the first results of the model and method are presented. In particular, the work focuses on a critical area of the education infrastructure that has suffered severely from the pandemic: classrooms. In two representative classroom scenarios (teaching and examination), the duration of stay for low risk of infection is investigated at different positions in the rooms for the case that one infectious person is present. The results qualitatively agree well with a documented outbreak in an elementary school but also show, in comparisons with other published data, how sensitive the assessment of the infection risk is to the amount of virus emitted on the individual amount of virus required for infection, as well as on the supply air volume. In this regard, the developed simulation model can be used as a useful virtual assessment for a detailed seat-related overview of the risk of infection, which is a significant advantage over established analytical models.

Modeling Clothing as a Vector for Transporting Airborne Particles and Pathogens across Indoor Microenvironments

Evidence suggests that human exposure to airborne particles and associated contaminants, including respiratory pathogens, can persist beyond a single microenvironment. By accumulating such contaminants from air, clothing may function as a transport vector and source of "secondary exposure". To investigate this function, a novel microenvironmental exposure modeling framework (ABICAM) was developed. This framework was applied to a para-occupational exposure scenario involving the deposition of viable SARS-CoV-2 in respiratory particles (0.5-20 μm) from a primary source onto clothing in a nonhealthcare setting and subsequent resuspension and secondary exposure in a car and home. Variability was assessed through Monte Carlo simulations. The total volume of infectious particles on the occupant's clothing immediately after work was 4800 μm3 (5th-95th percentiles: 870-32 000 μm3). This value was 61% (5-95%: 17-300%) of the occupant's primary inhalation exposure in the workplace while unmasked. By arrival at the occupant's home after a car commute, relatively rapid viral inactivation on cotton clothing had reduced the infectious volume on clothing by 80% (5-95%: 26-99%). Secondary inhalation exposure (after work) was low in the absence of close proximity and physical contact with contaminated clothing. In comparison, the average primary inhalation exposure in the workplace was higher by about 2-3 orders of magnitude. It remains theoretically possible that resuspension and physical contact with contaminated clothing can occasionally transmit SARS-CoV-2 between humans.

Impact of the SARS-CoV-2 Delta Variant on the Psychological States and Health-Related Quality of Life in Patients With Crohn's Disease

Background

Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic first reported in Wuhan, China, several research on the psychological impact of the pandemic on patients with Crohn’s disease (CD) have been conducted. However, with the progression of the global pandemic and the emergence of the SARS-CoV-2 B.1.617.2 (Delta) variant, follow-up studies need to be performed to monitor the alterations of psychological status and health-related quality of life (HRQoL) among CD patients.

Aims

We aimed to evaluate the impact of the SARS-CoV-2 Delta variant on the mental health and life quality among the CD population and tried to explore potent risk factors.

Methods

This observational study included 153 CD patients who responded to our pre-designed self-reported questionnaire. Demographic, clinical, and psychological information were collected and analyzed.

Results

Quite a number of CD patients were confronted with different levels of anxiety and depression, with incidence of 28.10 and 31.37% for anxiety and depression, respectively. Compared with non-pandemic circumstances, the life quality of CD patients due to the present situation was more often compromised. Isolation [odds ratio (OR): 4.71, P = 0.007] was verified as a risk factor for anxiety while use of telemedicine could help relieve anxiety (OR: 0.22, P < 0.001). Worsening of symptoms (OR: 4.92, P = 0.006), isolation (OR: 5.75, P = 0.005), and drug withdrawn (OR: 2.66, P = 0.026) were identified to be independent factors for developing depression. Likewise, use of telemedicine (OR: 0.13, P < 0.001) was negatively related to depression. Considering life quality, vaccination (OR: 3.07, P = 0.021) together with no medication (OR: 7.73, P = 0.010) was relevant to better life quality while worsening of symptoms (OR: 0.09, P = 0.034) were an independent risk factor for impaired life quality.

Conclusion

Many CD patients suffered from symptoms of anxiety and depression and impaired life quality during the COVID-19 pandemic. Those in isolation or with worsening of symptoms and drug withdrawn were more prone to experience psychological stress. Individualized management such as drug delivery and telemedicine should be promoted to maintain control of mental health and life quality during the pandemic.

Risk of SARS-CoV-2 in a car cabin assessed through 3D CFD simulations

In this study, the risk of infection from SARS-CoV-2 Delta variant of passengers sharing a car cabin with an infected subject for a 30-min journey is estimated through an integrated approach combining a recently developed predictive emission-to-risk approach and a validated CFD numerical model numerically solved using the open-source OpenFOAM software. Different scenarios were investigated to evaluate the effect of the infected subject position within the car cabin, the airflow rate of the HVAC system, the HVAC ventilation mode, and the expiratory activity (breathing vs. speaking). The numerical simulations here performed reveal that the risk of infection is strongly influenced by several key parameters: As an example, under the same ventilation mode and emitting scenario, the risk of infection ranges from zero to roughly 50% as a function of the HVAC flow rate. The results obtained also demonstrate that (i) simplified zero-dimensional approaches limit proper evaluation of the risk in such confined spaces, conversely, (ii) CFD approaches are needed to investigate the complex fluid dynamics in similar indoor environments, and, thus, (iii) the risk of infection in indoor environments characterized by fixed seats can be in principle controlled by properly designing the flow patterns of the environment.

The Global Epidemic of the SARS-CoV-2 Delta Variant, Key Spike Mutations and Immune Escape

During the COVID-19 pandemic, SARS-CoV-2 variants have emerged and spread worldwide. The Delta (B.1.617.2) variant was first reported in India in October 2020 and was classified as a "variant of concern (VOC)" by the WHO on 11 May, 2021. Compared to the wild-type strain, several studies have shown that the Delta variant is more transmissible and has higher viral loads in infected samples. COVID-19 patients infected with the Delta variant have a higher risk of hospitalization, intensive care unit (ICU) admission, and mortality. The Delta variant is becoming the dominant strain in many countries around the world. This review summarizes and analyses the biological characteristics of key amino acid mutations, the epidemic characteristics, and the immune escape of the Delta variant. We hope to provide scientific reference for the monitoring and prevention measures of the SARS-CoV-2 Delta variant and the development strategy of a second-generation vaccine.