Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events

Mechanistic Models of COVID-19: Insights into Disease Progression, Vaccines, and Therapeutics

The COVID-19 pandemic has severely impacted health systems and economies worldwide. Significant global efforts are therefore ongoing to improve vaccine efficacies, optimize vaccine deployment, and develop new antiviral therapies to combat the pandemic. Mechanistic viral dynamics and quantitative systems pharmacology models of SARS-CoV-2 infection, vaccines, immunomodulatory agents, and antiviral therapeutics have played a key role in advancing our understanding of SARS-CoV-2 pathogenesis and transmission, the interplay between innate and adaptive immunity to influence the outcomes of infection, effectiveness of treatments, mechanisms and performance of COVID-19 vaccines, and the impact of emerging SARS-CoV-2 variants. Here, we review some of the critical insights provided by these models and discuss the challenges ahead.

Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children

Systematic SARS-CoV-2 testing is a valuable tool for infection control and surveillance. However, broad application of high sensitive RT-qPCR testing in children is often hampered due to unpleasant sample collection, limited RT-qPCR capacities and high costs. Here, we developed a high-throughput approach (‘Lolli-Method’) for SARS-CoV-2 detection in children, combining non-invasive sample collection with an RT-qPCR-pool testing strategy. SARS-CoV-2 infections were diagnosed with sensitivities of 100% and 93.9% when viral loads were >10⁶ copies/ml and >10³ copies/ml in corresponding Naso-/Oropharyngeal-swabs, respectively. For effective application of the Lolli-Method in schools and daycare facilities, SEIR-modeling indicated a preferred frequency of two tests per week. The developed test strategy was implemented in 3,700 schools and 698 daycare facilities in Germany, screening over 800,000 individuals twice per week. In a period of 3 months, 6,364 pool-RT-qPCRs tested positive (0.64%), ranging from 0.05% to 2.61% per week. Notably, infections correlated with local SARS-CoV-2 incidences and with a school social deprivation index. Moreover, in comparison with the alpha variant, statistical modeling revealed a 36.8% increase for multiple (≥2 children) infections per class following infections with the delta variant. We conclude that the Lolli-Method is a powerful tool for SARS-CoV-2 surveillance and can support infection control in schools and daycare facilities.

Dewald et al. combine a non-invasive sampling approach (Lolli-Test) with an RT qPCR-pool testing strategy to screen for SARS-CoV-2 infections in children and use the method for surveillance and infection control in > 4000 school and daycare settings.

Nationwide Harmonization Effort for Semi-Quantitative Reporting of SARS-CoV-2 PCR Test Results in Belgium

From early 2020, a high demand for SARS-CoV-2 tests was driven by several testing indications, including asymptomatic cases, resulting in the massive roll-out of PCR assays to combat the pandemic. Considering the dynamic of viral shedding during the course of infection, the demand to report cycle threshold (Ct) values rapidly emerged. As Ct values can be affected by a number of factors, we considered that harmonization of semi-quantitative PCR results across laboratories would avoid potential divergent interpretations, particularly in the absence of clinical or serological information. A proposal to harmonize reporting of test results was drafted by the National Reference Centre (NRC) UZ/KU Leuven, distinguishing four categories of positivity based on RNA copies/mL. Pre-quantified control material was shipped to 124 laboratories with instructions to setup a standard curve to define thresholds per assay. For each assay, the mean Ct value and corresponding standard deviation was calculated per target gene, for the three concentrations (107, 105 and 103 copies/mL) that determine the classification. The results of 17 assays are summarized. This harmonization effort allowed to ensure that all Belgian laboratories would report positive PCR results in the same semi-quantitative manner to clinicians and to the national database which feeds contact tracing interventions.

Finding the infectious dose for COVID-19 by applying an airborne-transmission model to superspreader events

We probed the transmission of COVID-19 by applying an airborne transmission model to five well-documented case studies—a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. For all events the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. Applying the model to those events yields results that suggest the following: (1) transmission was airborne; (2) superspreading events do not require an index patient with an unusually high viral load; (3) the viral loads for all of the index patients were of the same order of magnitude and consistent with experimentally measured values for patients at the onset of symptoms, even though viral loads across the population vary by a factor of >10⁸. In particular we used a Wells-Riley exposure model to calculate q, the total average number of infectious quanta inhaled by a person at the event. Given the q value for each event, the simple airborne transmission model was used to determined S_q, the rate at which the index patient exhaled infectious quanta and N₀, the characteristic number of COVID-19 virions needed to induce infection. Despite the uncertainties in the values of some parameters of the superspreading events, all five events yielded (N₀∼300–2,000 virions), which is similar to published values for influenza. Finally, this work describes the conditions under which similar methods can provide actionable information on the transmission of other viruses.

Mitigation of SARS-CoV-2 transmission at a large public university

In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.

Mitigation of SARS-CoV-2 transmission at a large public university

In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.

Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.

Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.

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

The Delta variant of SARS-CoV-2 causes higher viral loads in infected hosts, increasing the risk of close proximity airborne transmission through breathing, speaking and coughing. We performed a Monte Carlo simulation using a social contact network and exponential dose-response model to quantify the close proximity reproduction number of both wild-type SARS-CoV-2 and the Delta variant. We estimate more than twice as many Delta variant cases will reproduce infection in their close proximity contacts (64%) versus the wild-type SARS-CoV-2 (29%). Occupational health guidelines must consider close proximity airborne transmission and recommend improved personal respiratory protection for high-risk workers.

Multi-scale modelling reveals that early super-spreader events are a likely contributor to novel variant predominance

The emergence of new SARS-CoV-2 variants of concern (VOC) has hampered international efforts to contain the COVID-19 pandemic. VOCs have been characterized to varying degrees by higher transmissibility, worse infection outcomes and evasion of vaccine and infection-induced immunologic memory. VOCs are hypothesized to have originated from animal reservoirs, communities in regions with low surveillance and/or single individuals with poor immunologic control of the virus. Yet, the factors dictating which variants ultimately predominate remain incompletely characterized. Here we present a multi-scale model of SARS-CoV-2 dynamics that describes population spread through individuals whose viral loads and numbers of contacts (drawn from an over-dispersed distribution) are both time-varying. This framework allows us to explore how super-spreader events (SSE) (defined as greater than five secondary infections per day) contribute to variant emergence. We find stochasticity remains a powerful determinant of predominance. Variants that predominate are more likely to be associated with higher infectiousness, an SSE early after variant emergence and ongoing decline of the current dominant variant. Additionally, our simulations reveal that most new highly infectious variants that infect one or a few individuals do not achieve permanence in the population. Consequently, interventions that reduce super-spreading may delay or mitigate emergence of VOCs.

SARS-CoV-2 Transmission Risk Model in an Urban Area of Mexico, Based on GIS Analysis and Viral Load

The COVID-19 pandemic highlighted health systems vulnerabilities, as well as thoughtlessness by governments and society. Due to the nature of this contingency, the use of geographic information systems (GIS) is essential to understand the SARS-CoV-2 distribution dynamics within a defined geographic area. This work was performed in Tepic, a medium-sized city in Mexico. The residence of 834 COVID-19 infected individuals was georeferenced and categorized by viral load (Ct). The analysis took place during the maximum contagion of the first four waves of COVID-19 in Mexico, analyzing 158, 254, 143, and 279 cases in each wave respectively. Then heatmaps were built and categorized into five areas ranging from very low to very high risk of contagion, finding that the second wave exhibited a greater number of cases with a high viral load. Additionally, a spatial analysis was performed to measure urban areas with a higher risk of contagion, during this wave this area had 19,203.08 km² (36.11% of the city). Therefore, a kernel density spatial model integrated by meaningful variables such as the number of infected subjects, viral load, and place of residence in cities, to establish geographic zones with different degrees of infection risk, could be useful for decision-making in future epidemic events.

The changing epidemiology of SARS-CoV-2

We have come a long way since the start of the COVID-19 pandemic-from hoarding toilet paper and wiping down groceries to sending our children back to school and vaccinating billions. Over this period, the global community of epidemiologists and evolutionary biologists has also come a long way in understanding the complex and changing dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19. In this Review, we retrace our steps through the questions that this community faced as the pandemic unfolded. We focus on the key roles that mathematical modeling and quantitative analyses of empirical data have played in allowing us to address these questions and ultimately to better understand and control the pandemic.

Matrix-Assisted Laser Desorption and Ionization Time-of-Flight Mass Spectrometry Analysis for the Direct Detection of SARS-CoV-2 in Nasopharyngeal Swabs

The most common diagnostic method used for coronavirus disease-2019 (COVID-19) is real-time reverse transcription polymerase chain reaction (PCR). However, it requires complex and labor-intensive procedures and involves excessive positive results derived from viral debris. We developed a method for the direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs, which uses matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-ToF MS) to identify specific peptides from the SARS-CoV-2 nucleocapsid phosphoprotein (NP). SARS-CoV-2 viral particles were separated from biological molecules in nasopharyngeal swabs by an ultrafiltration cartridge. Further purification was performed by an anion exchange resin, and purified NP was digested into peptides using trypsin. The peptides from SARS-CoV-2 that were inoculated into nasopharyngeal swabs were detected by MALDI-ToF MS, and the limit of detection was 10^6.7 viral copies. This value equates to 10^7.9 viral copies per swab and is approximately equivalent to the viral load of contagious patients. Seven NP-derived peptides were selected as the target molecules for the detection of SARS-CoV-2 in clinical specimens. The method detected between two and seven NP-derived peptides in 19 nasopharyngeal swab specimens from contagious COVID-19 patients. These peptides were not detected in four specimens in which SARS-CoV-2 RNA was not detected by PCR. Mutated NP-derived peptides were found in some specimens, and their patterns of amino acid replacement were estimated by accurate mass. Our results provide evidence that the developed MALDI-ToF MS-based method in a combination of straightforward purification steps and a rapid detection step directly detect SARS-CoV-2-specific peptides in nasopharyngeal swabs and can be a reliable high-throughput diagnostic method for COVID-19.

Clinical performance of the Roche Elecsys SARS-CoV-2 antigen fully automated electrochemiluminescence immunoassay

Objective

We assessed the clinical performance of novel Roche Elecsys SARS-CoV-2 Antigen fully automated electrochemiluminescence immunoassay (ECLIA).

Design and methods

We tested 160 subjects, 110 (68.8%), with positive molecular test for SARS-CoV-2 infection in nasopharyngeal samples, with Altona Diagnostics RealStar SARS-CoV-2 RT-PCR Kit and Roche Elecsys SARS-CoV-2 Antigen.

Results

Highly significant correlation was found between Elecsys SARS-CoV-2 Antigen ECLIA and cycle threshold (Ct) values of SARS-CoV-2 S and E genes (both r = −0.91; p < 0.001). The area under the curve (AUC), sensitivity and specificity of Elecsys SARS-CoV-2 Antigen ECLIA were 0.83, 0.43 and 1.00 in all samples, 0.99, 0.87 and 0.99 in those with both Ct values < 30, as well as 1.00, 1.00 and 0.89 in samples with both Ct values < 25.

Conclusion

Roche Elecsys SARS-CoV-2 Antigen ECLIA may be a surrogate of molecular testing for identification of super-spreaders.

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.

Sample-to-answer, extraction-free, real-time RT-LAMP test for SARS-CoV-2 in nasopharyngeal, nasal, and saliva samples: Implications and use for surveillance testing

The global COVID-19 pandemic has highlighted the need for rapid, accurate and accessible nucleic acid tests to enable timely identification of infected individuals. We optimized a sample-to-answer nucleic acid test for SARS-CoV-2 that provides results in <1 hour using inexpensive and readily available reagents. The test workflow includes a simple lysis and viral inactivation protocol followed by direct isothermal amplification of viral RNA using RT-LAMP. The assay was validated using two different instruments, a portable isothermal fluorimeter and a standard thermocycler. Results of the RT-LAMP assay were compared to traditional RT-qPCR for nasopharyngeal swabs, nasal swabs, and saliva collected from a cohort of patients hospitalized due to COVID-19. For all three sample types, positive agreement with RT-LAMP performed using the isothermal fluorimeter was 100% for samples with Ct <30 and 69-91% for samples with Ct <40. Following validation, the test was successfully scaled to test the saliva of up to 400 asymptomatic individuals per day as part of the campus surveillance program at Rice University. Successful development, validation, and scaling of this sample-to-answer, extraction-free real-time RT-LAMP test for SARS-CoV-2 adds a highly adaptable tool to efforts to control the COVID-19 pandemic, and can inform test development strategies for future infectious disease threats.

Comparing the impact of vaccination strategies on the spread of COVID-19, including a novel household-targeted vaccination strategy

With limited availability of vaccines, an efficient use of the limited supply of vaccines in order to achieve herd immunity will be an important tool to combat the wide-spread prevalence of COVID-19. Here, we compare a selection of strategies for vaccine distribution, including a novel targeted vaccination approach (EHR) that provides a noticeable increase in vaccine impact on disease spread compared to age-prioritized and random selection vaccination schemes. Using high-fidelity individual-based computer simulations with Oslo, Norway as an example, we find that for a community reproductive number in a setting where the base pre-vaccination reproduction number R = 2.1 without population immunity, the EHR method reaches herd immunity at 48% of the population vaccinated with 90% efficiency, whereas the common age-prioritized approach needs 89%, and a population-wide random selection approach requires 61%. We find that age-based strategies have a substantially weaker impact on epidemic spread and struggle to achieve herd immunity under the majority of conditions. Furthermore, the vaccination of minors is essential to achieving herd immunity, even for ideal vaccines providing 100% protection.

Digital CRISPR/Cas12b-based platform enabled absolute quantification of viral RNA

Early and accurate diagnosis of viruses is critical for control of the pandemic. CRISPR/Cas-based detection of nucleic acid is an emerging technology for molecular diagnostics, and has been applied for virus detection. Though these methods have excellent sensitivity and specificity, most of them were not able to measure the quantity of virus. We here developed a droplet digital reverse transcription loop-mediated isothermal amplification (RT-LAMP) enhanced Cas12b-based RNA detection platform (RECD), for quantitative detection of viral RNA. CRISPR/Cas12b, which is more thermally stable than other family members in CRISPR systems, is combined with digital RT-LAMP. Due to the innate characteristic of digital format detection and CRISPR/Cas system, droplet digital RECD (ddRECD) assay enables absolute quantification of viral RNA, with single-molecule sensitivity. We expect the ddRECD assay will be a powerful tool for molecular diagnostics.

COVID-19: Testing Landscape Post-Infection, -Vaccination, and Future Perspectives

On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19) outbreak a global pandemic. Although molecular testing remains the gold standard for COVID-19 diagnosis, serological testing enables the evaluation of the immune response to severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection and vaccination, and can be used to assess community viral spread. This review summarizes and analyzes the current landscape of SARS-CoV-2 testing in the United States and includes guidance on both when and why it is important to use direct pathogen detection and/or serological testing. The usefulness of monitoring humoral and cellular immune responses in infected and vaccinated patients is also addressed. Finally, this review considers current challenges, future perspectives for SARS-CoV-2 testing, and how diagnostics are being adapted as the virus evolves.

Critical literature review and pooled analysis of diagnostic accuracy of Ortho VITROS SARS-CoV-2 antigen test for diagnosing acute SARS-CoV-2 infections

Background: The present study is aimed at reviewing and meta-analyzing the currently published data on the diagnostic accuracy of Ortho VITROS SARS-CoV-2 antigen test for diagnosing acute SARS-CoV-2 infections. Methods: An electronic search was conducted in Scopus and Medline with the keywords "VITROS" AND "antigen" AND "COVID-19" OR "SARS-CoV-2" AND "immunoassay" within the search fields "TITLE" AND "ABSTRACT" AND "KEYWORDS", without no date (i.e., up to January 23, 2022) or language restrictions, aimed at detecting documents reporting the diagnostic accuracy of this SARSCoV-2 immunoassay compared with reference molecular diagnostic methods. Results: Overall, 5 studies (n=2734 samples) were finally included in our pooled analysis, four of which also provided diagnostic sensitivity in oro-and nasopharyngeal samples with high viral load. The pooled cumulative diagnostic sensitivity and specificity were 0.82 (95%CI, 0.78-0.86) and 1.00 (95%CI, 1.00-1.00), respectively, whilst the area under the curve was 0.995 (95%CI, 0.993-0.997), the cumulative agreement 97.2% (95%CI, 96.5-97.8%), with 0.89 (95%CI, 0.86-0.91) kappa statistics, thus reflecting an almost perfect concordance with reference molecular biology techniques. The pooled diagnostic sensitivity in samples with high viral load was as high as 0.98 (95%CI, 0.96-0.99). Conclusions: These results confirm that the automated and high-throughput Ortho VITROS SARS-CoV-2 antigen test may represent a valuable surrogate of molecular testing for diagnosing acute SARS-CoV-2 infections, especially in subjects with high viral load.

Identification of a therapeutic interfering particle-A single-dose SARS-CoV-2 antiviral intervention with a high barrier to resistance

Viral-deletion mutants that conditionally replicate and inhibit the wild-type virus (i.e., defective interfering particles, DIPs) have long been proposed as single-administration interventions with high genetic barriers to resistance. However, theories predict that robust, therapeutic DIPs (i.e., therapeutic interfering particles, TIPs) must conditionally spread between cells with R0 >1. Here, we report engineering of TIPs that conditionally replicate with SARS-CoV-2, exhibit R0 >1, and inhibit viral replication 10- to 100-fold. Inhibition occurs via competition for viral replication machinery, and a single administration of TIP RNA inhibits SARS-CoV-2 sustainably in continuous cultures. Strikingly, TIPs maintain efficacy against neutralization-resistant variants (e.g., B.1.351). In hamsters, both prophylactic and therapeutic intranasal administration of lipid-nanoparticle TIPs durably suppressed SARS-CoV-2 by 100-fold in the lungs, reduced pro-inflammatory cytokine expression, and prevented severe pulmonary edema. These data provide proof of concept for a class of single-administration antivirals that may circumvent current requirements to continually update medical countermeasures against new variants.

In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness

The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person's infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop viral dynamic models of SARS-CoV-2 infection and fit them to data to estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness and show a person's infectiousness increases sublinearly with VL and that the logarithm of the VL in the upper respiratory tract is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and RT-PCR tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.

"Evaluation of methylene blue based photodynamic inactivation (PDI) against intracellular B-CoV and SARS-CoV2 viruses under different light sources in vitro as a basis for new local treatment strategies in the early phase of a Covid19 infection"

The local antiviral photodynamic inactivation (PDI) may prove to be a helpful tool reducing the viral load in the nose and throat area in the early phase of a Covid19 infection. Both the infectivity and the prognosis of SARS-CoV-2 infections in the early phase can depend on the viral load in this area. The aim of our study was to find a simplified PDI therapy option against corona viruses in this region with low dose methylene blue (MB) as photosensitizer and use of LED light instead of laser. As a substitute for SARS-CoV2 viruses we started with BCoV infected U373 cells first. We used an 810nm diode laser with 300mW/cm2 and 100J/cm² light dose as well as a 590 nm LED and a broadband LED with irradiation intensity of 10,000 lx each (irradiation time 2.5 and 10 min) and concentrations of the sensitizer of 0.001% and 0.0001%. The 0.001% MB sensitizer experiments showed similar results with all exposures. The logarithmic reduction factor varied between ≥ 5.29 and ≥ 5.31, (0.001% MB sensitizer) and ≥ 4.6 and ≥ 5.31 (0.0001% MB) respectively. Extending the LED irradiation time from 2 to 5 and 10 minutes did not change these results. In contrast approaches of BCoV-infected cells in the dark, treated with 0.001% and 0.0001% MB sensitizer alone, a lot of residual viruses could be detected after 10 minutes of incubation (RF 0.9 and RF 1.23 for 0.001% MB and 0.0001% MB respectively) In our SARS-CoV-2 experiments with VERO E6 infected cells the irradiation time was reduced to 1, 2 and 3 minutes for both concentrations with increasing broadband LED radiation intensity from 20 to 50 and 100.000 lx. (RF 4.67 for 0.001% and 0.0001% respectively). This showed a minimum concentration of 0.0001%MB and a minimum radiation intensity of 20,000 lx leads to a 99.99% reduction of intracellular and extracellular viruses after one minute exposure.

The vaccination threshold for SARS-CoV-2 depends on the indoor setting and room ventilation

BACKGROUND

Effective vaccines are now available for SARS-CoV-2 in the 2nd year of the COVID-19 pandemic, but there remains significant uncertainty surrounding the necessary vaccination rate to safely lift occupancy controls in public buildings and return to pre-pandemic norms. The aim of this paper is to estimate setting-specific vaccination thresholds for SARS-CoV-2 to prevent sustained community transmission using classical principles of airborne contagion modeling. We calculated the airborne infection risk in three settings, a classroom, prison cell block, and restaurant, at typical ventilation rates, and then the expected number of infections resulting from this risk at varying percentages of occupant immunity.

RESULTS

We estimate the setting-specific immunity threshold for control of wild-type SARS-CoV-2 to range from a low of 40% for a mechanically ventilation classroom to a high of 85% for a naturally ventilated restaurant.

CONCLUSIONS

If vaccination rates are limited to a theoretical minimum of approximately two-thirds of the population, enhanced ventilation above minimum standards for acceptable air quality is needed to reduce the frequency and severity of SARS-CoV-2 superspreading events in high-risk indoor environments.

Analysis of efficacy of intervention strategies for COVID-19 transmission: A case study of Hong Kong

By the end of February 2021, COVID-19 had spread to over 230 countries, with more than 100 million confirmed cases and 2.5 million deaths. To control infection spread with the least disruption to economic and societal activities, it is crucial to implement the various interventions effectively. In this study, we developed an agent-based SEIR model, using real demographic and geographic data from Hong Kong, to analyse the efficiency of various intervention strategies in preventing infection by the SARS-CoV-2 virus. Close contact route including short-range airborne is considered as the main transmission routes for COVID-19 spread. Contact tracing is not that useful if all other interventions have been fully deployed. The number of infected individuals could be halved if people reduced their close contact rate by 25%. For reducing transmission, students should be prioritized for vaccination rather than retired older people and preschool aged children. Home isolation, and taking the nucleic acid test (NAT) as soon as possible after symptom onset, are much more effective interventions than wearing masks in public places. Temperature screening in public places only disrupted the infection spread by a small amount when other interventions have been fully implemented. Our results may be useful for other highly populated cities, when choosing their intervention strategies to prevent outbreaks of COVID-19 and similar diseases.

Estimating salivary carriage of severe acute respiratory syndrome coronavirus 2 in nonsymptomatic people and efficacy of mouthrinse in reducing viral load: A randomized controlled trial

Background

Many people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) never develop substantial symptoms. With more than 34 million people in the United States already infected and highly transmissible variants rapidly emerging, it is highly probable that post- and presymptomatic people will form an important fraction of those seeking dental care. Salivary carriage rates in these populations are not known. Moreover, although preventing transmission is critical for controlling spread, the efficacy of mouthrinses in reducing oral viral load is poorly studied.

Methods

The authors recruited 201 asymptomatic, presymptomatic, postsymptomatic, and symptomatic people and measured copy numbers of SARS-CoV-2 in unstimulated saliva using real-time reverse transcriptase quantitative polymerase chain reaction. Subsequently, the authors inducted 41 symptomatic people into a randomized, triple-blinded study and instructed them to rinse with saline, 1% hydrogen peroxide, 0.12% chlorhexidine, or 0.5% povidone-iodine for 60 seconds. The authors measured viral load 15 and 45 minutes after rinsing.

Results

Salivary SARS-CoV-2 was detected in 23% of asymptomatic, 60% of postsymptomatic, and 28% of presymptomatic participants. Neither carriage rate nor viral load correlated with COVID-19 symptomatology, age, sex, or race or ethnicity. All 4 mouthrinses decreased viral load by 61% through 89% at 15 minutes and by 70% through 97% at 45 minutes. The extent of reduction correlated significantly with initial viral load.

Conclusions

Nonsymptomatic people can pose a risk of transmitting the virus, and mouthrinses are simple and efficacious means of reducing this risk, especially when the load is less than 10⁴ copies per milliliter.

Practical Implications

At a time when resources are stretched, the findings of this study contribute to evidence-based selection of personal protection equipment and simple infection-control practices to reduce contagion at source.

This clinical trial was registered at ClinicalTrials.gov. The registration number is NCT04603794.

Superspreading in the emergence of COVID-19 variants

Superspreading and variants of concern (VOC) of the human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the main catalyzers of the coronavirus disease 2019 (COVID-19) pandemic. However, measuring their individual impact is challenging. By examining the largest database of SARS-CoV-2 genomes The Global Initiative on Sharing Avian Influenza Data [GISAID; n >1.2 million high-quality (HQ) sequences], we present evidence suggesting that superspreading has had a key role in the epidemiological predominance of VOC. There are clear signatures in the database compatible with large superspreading events (SSEs) coinciding chronologically with the worst epidemiological scenarios triggered by VOC. The data suggest that, without the randomness effect of the genetic drift facilitated by superspreading, new VOC of SARS-CoV-2 would have had more limited chance of success.

Mathematical Modeling of Vaccines That Prevent SARS-CoV-2 Transmission

SARS-CoV-2 vaccine clinical trials assess efficacy against disease (VEDIS), the ability to block symptomatic COVID-19. They only partially discriminate whether VEDIS is mediated by preventing infection completely, which is defined as detection of virus in the airways (VESUSC), or by preventing symptoms despite infection (VESYMP). Vaccine efficacy against transmissibility given infection (VEINF), the decrease in secondary transmissions from infected vaccine recipients, is also not measured. Using mathematical modeling of data from King County Washington, we demonstrate that if the Moderna (mRNA-1273QS) and Pfizer-BioNTech (BNT162b2) vaccines, which demonstrated VEDIS > 90% in clinical trials, mediate VEDIS by VESUSC, then a limited fourth epidemic wave of infections with the highly infectious B.1.1.7 variant would have been predicted in spring 2021 assuming rapid vaccine roll out. If high VEDIS is explained by VESYMP, then high VEINF would have also been necessary to limit the extent of this fourth wave. Vaccines which completely protect against infection or secondary transmission also substantially lower the number of people who must be vaccinated before the herd immunity threshold is reached. The limited extent of the fourth wave suggests that the vaccines have either high VESUSC or both high VESYMP and high VEINF against B.1.1.7. Finally, using a separate intra-host mathematical model of viral kinetics, we demonstrate that a 0.6 log vaccine-mediated reduction in average peak viral load might be sufficient to achieve 50% VEINF, which suggests that human challenge studies with a relatively low number of infected participants could be employed to estimate all three vaccine efficacy metrics.

SARS-CoV-2 Seroprevalence Structure of the Russian Population during the COVID-19 Pandemic

The SARS-CoV-2 pandemic, which came to Russia in March 2020, is accompanied by morbidity level changes and can be tracked using serological monitoring of a representative population sample from Federal Districts (FDs) and individual regions. In a longitudinal cohort study conducted in 26 model regions of Russia, distributed across all FDs, we investigated the distribution and cumulative proportions of individuals with antibodies (Abs) to the SARS-CoV-2 nucleocapsid antigen (Ag), in the period from June to December 2020, using a three-phase monitoring process. In addition, during the formation of the cohort of volunteers, the number of seropositive convalescents, persons who had contact with patients or COVID-19 convalescents, and the prevalence of asymptomatic forms of infection among seropositive volunteers were determined. According to a uniform methodology, 3 mL of blood was taken from the examined individuals, and plasma was separated, from which the presence of Abs to nucleocapsid Ag was determined on a Thermo Scientific Multiascan FC device using the "ELISA anti-SARS-CoV-2 IgG" reagent set (prod. Scientific Center for Applied Microbiology and Biotechnology), in accordance with the developer's instructions. Volunteers (74,158) were surveyed and divided into seven age groups (1-17, 18-29, 30-39, 40-49, 59-59, 60-69, and 70+ years old), among whom 14,275 were identified as having antibodies to SARS-CoV-2. The average percent seropositive in Russia was 17.8% (IQR: 8.8-23.2). The largest proportion was found among children under 17 years old (21.6% (IQR: 13.1-31.7). In the remaining groups, seroprevalence ranged from 15.6% (IQR: 8-21.1) to 18.0% (IQR: 13.4-22.6). During monitoring, three (immune) response groups were found: (A) groups with a continuous increase in the proportion of seropositive; (B) those with a slow rate of increase in seroprevalence; and (C) those with a two-phase curve, wherein the initial increase was replaced by a decrease in the percentage of seropositive individuals. A significant correlation was revealed between the number of COVID-19 convalescents and contact persons, and between the number of contacts and healthy seropositive volunteers. Among the seropositive volunteers, more than 93.6% (IQR: 87.1-94.9) were asymptomatic. The results show that the COVID-19 pandemic is accompanied by an increase in seroprevalence, which may be important for the formation of herd immunity.

SARS-CoV-2 Seroprevalence Structure of the Russian Population during the COVID-19 Pandemic

The SARS-CoV-2 pandemic, which came to Russia in March 2020, is accompanied by morbidity level changes and can be tracked using serological monitoring of a representative population sample from Federal Districts (FDs) and individual regions. In a longitudinal cohort study conducted in 26 model regions of Russia, distributed across all FDs, we investigated the distribution and cumulative proportions of individuals with antibodies (Abs) to the SARS-CoV-2 nucleocapsid antigen (Ag), in the period from June to December 2020, using a three-phase monitoring process. In addition, during the formation of the cohort of volunteers, the number of seropositive convalescents, persons who had contact with patients or COVID-19 convalescents, and the prevalence of asymptomatic forms of infection among seropositive volunteers were determined. According to a uniform methodology, 3 mL of blood was taken from the examined individuals, and plasma was separated, from which the presence of Abs to nucleocapsid Ag was determined on a Thermo Scientific Multiascan FC device using the “ELISA anti-SARS-CoV-2 IgG” reagent set (prod. Scientific Center for Applied Microbiology and Biotechnology), in accordance with the developer’s instructions. Volunteers (74,158) were surveyed and divided into seven age groups (1–17, 18–29, 30–39, 40–49, 59–59, 60–69, and 70+ years old), among whom 14,275 were identified as having antibodies to SARS-CoV-2. The average percent seropositive in Russia was 17.8% (IQR: 8.8–23.2). The largest proportion was found among children under 17 years old (21.6% (IQR: 13.1–31.7). In the remaining groups, seroprevalence ranged from 15.6% (IQR: 8–21.1) to 18.0% (IQR: 13.4–22.6). During monitoring, three (immune) response groups were found: (A) groups with a continuous increase in the proportion of seropositive; (B) those with a slow rate of increase in seroprevalence; and (C) those with a two-phase curve, wherein the initial increase was replaced by a decrease in the percentage of seropositive individuals. A significant correlation was revealed between the number of COVID-19 convalescents and contact persons, and between the number of contacts and healthy seropositive volunteers. Among the seropositive volunteers, more than 93.6% (IQR: 87.1–94.9) were asymptomatic. The results show that the COVID-19 pandemic is accompanied by an increase in seroprevalence, which may be important for the formation of herd immunity.

Sub-spreading events limit the reliable elimination of heterogeneous epidemics

We show that sub-spreading events, i.e. transmission events in which an infection propagates to few or no individuals, can be surprisingly important for defining the lifetime of an infectious disease epidemic and hence its waiting time to elimination or fade-out, measured from the time-point of its last observed case. While limiting super-spreading promotes more effective control when cases are growing, we find that when incidence is waning, curbing sub-spreading is more important for achieving reliable elimination of the epidemic. Controlling super-spreading in this low-transmissibility phase offers diminishing returns over non-selective, population-wide measures. By restricting sub-spreading, we efficiently dampen remaining variations among the reproduction numbers of infectious events, which minimizes the risk of premature and late end-of-epidemic declarations. Because case-ascertainment or reporting rates can be modelled in exactly the same way as control policies, we concurrently show that the under-reporting of sub-spreading events during waning phases will engender overconfident assessments of epidemic elimination. While controlling sub-spreading may not be easily realized, the likely neglecting of these events by surveillance systems could result in unexpectedly risky end-of-epidemic declarations. Super-spreading controls the size of the epidemic peak but sub-spreading mediates the variability of its tail.

Real-world assessment of Fluorecare SARS-CoV-2 Spike Protein Test Kit

Objectives

Since commercial SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) antigen rapid detection tests (Ag-RDTs) display broad diagnostic efficiency, this study aimed to evaluate the clinical performance of Fluorecare SARS-CoV-2 Spike Protein Test Kit in a real-life scenario.

Methods

The study population consisted of a series of patients undergoing SARS-Cov-2 diagnostic testing at Pederzoli Hospital of Peschiera del Garda (Verona, Italy). A nasopharyngeal swab was collected upon hospital admission and assayed with molecular (Altona Diagnostics RealStar^® SARSCoV-2 RT-PCR Kit) and antigen (Fluorecare SARS-CoV-2 Spike Protein Test Kit) tests.

Results

The study population consisted of 354 patients (mean age, 47 ± 20 years; 195 women, 55.1%), 223 (65.8%) positive at molecular testing. A significant correlation was found between Fluorecare SARS-CoV-2 Spike Protein Test Kit and Altona (both S and E genes: r=-0.75; p<0.001). The cumulative area under the curve in all nasopharyngeal samples was 0.68. At ≥1.0 S/CO manufacturer's cut-off, the sensitivity, specificity, negative and positive predictive values were 27.5, 99.2, 41.5 and 98.5%, respectively. Considerable improvement of sensitivity was observed as Ct values decreased, becoming 66.7% in samples with mean Ct values <30, 90.5% in those with mean Ct values <25, up to 100% in those with mean Ct values <20.

Conclusions

The modest sensitivity and negative predictive value of Fluorecare SARS-CoV-2 Spike Protein Test Kit makes unadvisable to use this assay as surrogate of molecular testing for definitively diagnosing SARS-CoV-2 infection, though its suitable sensitivity at high viral load could make it a reliable screening test for patients with higher infective potential.

Revisiting the guidelines for ending isolation for COVID-19 patients

Since the start of the COVID-19 pandemic, two mainstream guidelines for defining when to end the isolation of SARS-CoV-2-infected individuals have been in use: the one-size-fits-all approach (i.e. patients are isolated for a fixed number of days) and the personalized approach (i.e. based on repeated testing of isolated patients). We use a mathematical framework to model within-host viral dynamics and test different criteria for ending isolation. By considering a fixed time of 10 days since symptom onset as the criterion for ending isolation, we estimated that the risk of releasing an individual who is still infectious is low (0-6.6%). However, this policy entails lengthy unnecessary isolations (4.8-8.3 days). In contrast, by using a personalized strategy, similar low risks can be reached with shorter prolonged isolations. The obtained findings provide a scientific rationale for policies on ending the isolation of SARS-CoV-2-infected individuals.

Heterogeneity matters: Contact structure and individual variation shape epidemic dynamics

In the recent COVID-19 pandemic, mathematical modeling constitutes an important tool to evaluate the prospective effectiveness of non-pharmaceutical interventions (NPIs) and to guide policy-making. Most research is, however, centered around characterizing the epidemic based on point estimates like the average infectiousness or the average number of contacts. In this work, we use stochastic simulations to investigate the consequences of a population's heterogeneity regarding connectivity and individual viral load levels. Therefore, we translate a COVID-19 ODE model to a stochastic multi-agent system. We use contact networks to model complex interaction structures and a probabilistic infection rate to model individual viral load variation. We observe a large dependency of the dispersion and dynamical evolution on the population's heterogeneity that is not adequately captured by point estimates, for instance, used in ODE models. In particular, models that assume the same clinical and transmission parameters may lead to different conclusions, depending on different types of heterogeneity in the population. For instance, the existence of hubs in the contact network leads to an initial increase of dispersion and the effective reproduction number, but to a lower herd immunity threshold (HIT) compared to homogeneous populations or a population where the heterogeneity stems solely from individual infectivity variations.

Correlations Between Olfactory Psychophysical Scores and SARS-CoV-2 Viral Load in COVID-19 Patients

Objectives/Hypothesis

The aim of this study was to evaluate the correlations between the severity and duration of olfactory dysfunctions (OD), assessed with psychophysical tests, and the viral load on the rhino‐pharyngeal swab determined with a direct method, in patients affected by coronavirus disease 2019 (COVID‐19).

Study design

Prospective cohort study.

Methods

Patients underwent psychophysical olfactory assessment with Connecticut Chemosensory Clinical Research Center test and determination of the normalized viral load on nasopharyngeal swab within 10 days of the clinical onset of COVID‐19.

Results

Sixty COVID‐19 patients were included in this study. On psychophysical testing, 12 patients (20% of the cohort) presented with anosmia, 11 (18.3%) severe hyposmia, 13 (18.3%) moderate hyposmia, and 10 (16.7%) mild hyposmia with an overall prevalence of OD of 76.7%. The overall median olfactory score was 50 (interquartile range [IQR] 30–72.5) with no significant differences between clinical severity subgroups. The median normalized viral load detected in the series was 2.56E+06 viral copies/10⁶ copies of human beta‐2microglobulin mRNA present in the sample (IQR 3.17E+04–1.58E+07) without any significant correlations with COVID‐19 severity. The correlation between viral load and olfactory scores at baseline (R² = 0.0007; P = .844) and 60‐day follow‐up (R² = 0.0077; P = .519) was weak and not significant.

Conclusions

The presence of OD does not seem to be useful in identifying subjects at risk for being super‐spreaders or who is at risk of developing long‐term OD. Similarly, the pathogenesis of OD is probably related to individual factors rather than to viral load and activity.

Level of Evidence

4 Laryngoscope, 131:2312–2318, 2021

Beyond the new normal: Assessing the feasibility of vaccine-based suppression of SARS-CoV-2

As the COVID-19 pandemic drags into its second year, there is hope on the horizon, in the form of SARS-CoV-2 vaccines which promise disease suppression and a return to pre-pandemic normalcy. In this study we critically examine the basis for that hope, using an epidemiological modeling framework to establish the link between vaccine characteristics and effectiveness in bringing an end to this unprecedented public health crisis. Our findings suggest that a return to pre-pandemic social and economic conditions without fully suppressing SARS-CoV-2 will lead to extensive viral spread, resulting in a high disease burden even in the presence of vaccines that reduce risk of infection and mortality. Our modeling points to the feasibility of complete SARS-CoV-2 suppression with high population-level compliance and vaccines that are highly effective at reducing SARS-CoV-2 infection. Notably, vaccine-mediated reduction of transmission is critical for viral suppression, and in order for partially-effective vaccines to play a positive role in SARS-CoV-2 suppression, complementary biomedical interventions and public health measures must be deployed simultaneously.

COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission

Widespread school closures occurred during the COVID-19 pandemic. Because closures are costly and damaging, many jurisdictions have since reopened schools with control measures in place. Early evidence indicated that schools were low risk and children were unlikely to be very infectious, but it is becoming clear that children and youth can acquire and transmit COVID-19 in school settings and that transmission clusters and outbreaks can be large. We describe the contrasting literature on school transmission, and argue that the apparent discrepancy can be reconciled by heterogeneity, or “overdispersion” in transmission, with many exposures yielding little to no risk of onward transmission, but some unfortunate exposures causing sizeable onward transmission. In addition, respiratory viral loads are as high in children and youth as in adults, pre- and asymptomatic transmission occur, and the possibility of aerosol transmission has been established. We use a stochastic individual-based model to find the implications of these combined observations for cluster sizes and control measures. We consider both individual and environment/activity contributions to the transmission rate, as both are known to contribute to variability in transmission. We find that even small heterogeneities in these contributions result in highly variable transmission cluster sizes in the classroom setting, with clusters ranging from 1 to 20 individuals in a class of 25. None of the mitigation protocols we modeled, initiated by a positive test in a symptomatic individual, are able to prevent large transmission clusters unless the transmission rate is low (in which case large clusters do not occur in any case). Among the measures we modeled, only rapid universal monitoring (for example by regular, onsite, pooled testing) accomplished this prevention. We suggest approaches and the rationale for mitigating these larger clusters, even if they are expected to be rare.

During the COVID-19 pandemic many jurisdictions closed schools in order to limit transmission of SARS-CoV-2. Because school closures are costly and damaging to students, schools were later reopened despite the risk of contact among students contributing to increased prevalence of the virus. Early data showed schools being mostly a low risk setting, but occasionally large outbreaks were observed. We argue that this heterogenous behaviour can be explained by variability in the rate of transmission, both at the level of the individual student and at the level of the classroom. We created a mathematical model of transmission in the classroom to explore the consequences of this variability for cluster size and control measures, considering what happens when a single infectious individual attends a classroom of susceptible students. We used the model to study different interventions with the aim of reducing the size of infection clusters, in situations where such clusters would be large. We found that interventions based on acting after symptomatic students receive a positive test, as is standard practice in many jurisdictions, are ineffective at preventing most infections, and instead found that only frequent screening of the entire class was able to reduce the size of clusters substantially.

Original Hosts, Clinical Features, Transmission Routes, and Vaccine Development for Coronavirus Disease (COVID-19)

The pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to public concern worldwide. Although a variety of hypotheses about the hosts of SARS-CoV-2 have been proposed, an exact conclusion has not yet been reached. Initial clinical manifestations associated with COVID-19 are similar to those of other acute respiratory infections, leading to misdiagnoses and resulting in the outbreak at the early stage. SARS-CoV-2 is predominantly spread by droplet transmission and close contact; the possibilities of fecal-oral, vertical, and aerosol transmission have not yet been fully confirmed or rejected. Besides, COVID-19 cases have been reported within communities, households, and nosocomial settings through contact with confirmed COVID-19 patients or asymptomatic individuals. Environmental contamination is also a major driver for the COVID-19 pandemic. Considering the absence of specific treatment for COVID-19, it is urgent to decrease the risk of transmission and take preventive measures to control the spread of the virus. In this review, we summarize the latest available data on the potential hosts, entry receptors, clinical features, and risk factors of COVID-19 and transmission routes of SARS-CoV-2, and we present the data about development of vaccines.

Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies

SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient's infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient's progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.

In vivo kinetics of SARS-CoV-2 infection and its relationship with a person's infectiousness

The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person's infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop data-driven viral dynamic models of SARS-CoV-2 infection and estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking VL to infectiousness, showing that a person's infectiousness increases sub-linearly with VL. We show that the logarithm of the VL in the upper respiratory tract (URT) is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and reverse transcription polymerase chain reaction (RT-PCR) tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost, but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.

SIGNIFICANCE

Quantifying the kinetics of SARS-CoV-2 infection and individual infectiousness is key to quantitatively understanding SARS-CoV-2 transmission and evaluating intervention strategies. Here we developed data-driven within-host models of SARS-CoV-2 infection and by fitting them to clinical data we estimated key within-host viral dynamic parameters. We also developed a mechanistic model for viral transmission and show that the logarithm of the viral load in the upper respiratory tract serves an appropriate surrogate for a person's infectiousness. Using data on how viral load changes during infection, we further evaluated the effectiveness of PCR and antigen-based testing strategies for averting transmission and identifying infected individuals.

The SARS-CoV-2 viral load in COVID-19 patients is lower on face mask filters than on nasopharyngeal swabs

Face masks and personal respirators are used to curb the transmission of SARS-CoV-2 in respiratory droplets; filters embedded in some personal protective equipment could be used as a non-invasive sample source for applications, including at-home testing, but information is needed about whether filters are suited to capture viral particles for SARS-CoV-2 detection. In this study, we generated inactivated virus-laden aerosols of 0.3–2 microns in diameter (0.9 µm mean diameter by mass) and dispersed the aerosolized viral particles onto electrostatic face mask filters. The limit of detection for inactivated coronaviruses SARS-CoV-2 and HCoV-NL63 extracted from filters was between 10 to 100 copies/filter for both viruses. Testing for SARS-CoV-2, using face mask filters and nasopharyngeal swabs collected from hospitalized COVID-19-patients, showed that filter samples offered reduced sensitivity (8.5% compared to nasopharyngeal swabs). The low concordance of SARS-CoV-2 detection between filters and nasopharyngeal swabs indicated that number of viral particles collected on the face mask filter was below the limit of detection for all patients but those with the highest viral loads. This indicated face masks are unsuitable to replace diagnostic nasopharyngeal swabs in COVID-19 diagnosis. The ability to detect nucleic acids on face mask filters may, however, find other uses worth future investigation.

Clinical Assessment of the DiaSorin LIAISON SARS-CoV-2 Ag Chemiluminescence Immunoassay

BACKGROUND

Due to the large volume of tests needed in a relatively short time for screening and diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, antigen immunoassays may provide a potential supplement to molecular testing. This study was aimed to assess the clinical preference of DiaSorin LIAISON SARS-CoV-2 Ag chemiluminescence immunoassay.

METHODS

An upper respiratory specimen was collected in a series of patients referred to the Laboratory Medicine service of Pederzoli Hospital (Peschiera del Garda, Verona, Italy) for screening or diagnosis of SARS-CoV-2 infection. Nasopharyngeal samples were assayed with DiaSorin LIAISON SARS-CoV-2 Ag test and Altona Diagnostics RealStar^® SARS-CoV-2 RT-PCR Kit.

RESULTS

The final study population consisted of 421 patients (median age, 48 years; 227 women), 301 (71.5%) with positive result of molecular testing, and 126 (29.9%) with cycle threshold (Ct) values of both E and S genes <29.5, thus reflecting higher infectivity. The area under the curve of DiaSorin LIAISON SARS-CoV-2 Ag test 0.82 (95% CI, 0.79-0.86) for sample positivity and 0.98 for higher sample infectivity (95% CI, 0.97 to 0.99). The optimal cut-off for sample positivity was 82 TCID₅₀/mL (0.78 sensitivity, 0.73 specificity and 77% diagnostic accuracy), whilst that for identifying samples associated with a high infective risk was 106 TCID₅₀/mL (0.94 sensitivity, 0.96 specificity and 95% diagnostic accuracy).

CONCLUSION

The performance of this chemiluminescence immunoassay would not permit it to replace molecular testing for diagnosing SARS-CoV-2, but may enable rapid and efficient detection of subjects with high SARS-CoV-2 viral load, who are responsible for the largest proportion of infectious clusters.

Robust estimation of SARS-CoV-2 epidemic in US counties

The COVID-19 outbreak is asynchronous in US counties. Mitigating the COVID-19 transmission requires not only the state and federal level order of protective measures such as social distancing and testing, but also public awareness of time-dependent risk and reactions at county and community levels. We propose a robust approach to estimate the heterogeneous progression of SARS-CoV-2 at all US counties having no less than 2 COVID-19 associated deaths, and we use the daily probability of contracting (PoC) SARS-CoV-2 for a susceptible individual to quantify the risk of SARS-CoV-2 transmission in a community. We found that shortening by [Formula: see text] of the infectious period of SARS-CoV-2 can reduce around [Formula: see text] (or 78 K, [Formula: see text] CI: [66 K , 89 K ]) of the COVID-19 associated deaths in the US as of 20 September 2020. Our findings also indicate that reducing infection and deaths by a shortened infectious period is more pronounced for areas with the effective reproduction number close to 1, suggesting that testing should be used along with other mitigation measures, such as social distancing and facial mask-wearing, to reduce the transmission rate. Our deliverable includes a dynamic county-level map for local officials to determine optimal policy responses and for the public to better understand the risk of contracting SARS-CoV-2 on each day.

Slight reduction in SARS-CoV-2 exposure viral load due to masking results in a significant reduction in transmission with widespread implementation

Masks are a vital tool for limiting SARS-CoV-2 spread in the population. Here we utilize a mathematical model to assess the impact of masking on transmission within individual transmission pairs and at the population level. Our model quantitatively links mask efficacy to reductions in viral load and subsequent transmission risk. Our results reinforce that the use of masks by both a potential transmitter and exposed person substantially reduces the probability of successful transmission, even if masks only lower exposure viral load by ~ 50%. Slight increases in mask adherence and/or efficacy above current levels would reduce the effective reproductive number (R_e) substantially below 1, particularly if implemented comprehensively in potential super-spreader environments. Our model predicts that moderately efficacious masks will also lower exposure viral load tenfold among people who get infected despite masking, potentially limiting infection severity. Because peak viral load tends to occur pre-symptomatically, we also identify that antiviral therapy targeting symptomatic individuals is unlikely to impact transmission risk. Instead, antiviral therapy would only lower R_e if dosed as post-exposure prophylaxis and if given to ~ 50% of newly infected people within 3 days of an exposure. These results highlight the primacy of masking relative to other biomedical interventions under consideration for limiting the extent of the COVID-19 pandemic prior to widespread implementation of a vaccine. To confirm this prediction, we used a regression model of King County, Washington data and simulated the counterfactual scenario without mask wearing to estimate that in the absence of additional interventions, mask wearing decreased R_e from 1.3–1.5 to ~ 1.0 between June and September 2020.

Five approaches to the suppression of SARS-CoV-2 without intensive social distancing

Initial efforts to mitigate transmission of SARS-CoV-2 relied on intensive social distancing measures such as school and workplace closures, shelter-in-place orders and prohibitions on the gathering of people. Other non-pharmaceutical interventions for suppressing transmission include active case finding, contact tracing, quarantine, immunity or health certification, and a wide range of personal protective measures. Here we investigate the potential effectiveness of these alternative approaches to suppression. We introduce a conceptual framework represented by two mathematical models that differ in strategy. We find both strategies may be effective, although both require extensive testing and work within a relatively narrow range of conditions. Generalized protective measures such as wearing face masks, improved hygiene and local reductions in density are found to significantly increase the effectiveness of targeted interventions.

Mechanistic Modeling of SARS-CoV-2 and Other Infectious Diseases and the Effects of Therapeutics

Modern viral kinetic modeling and its application to therapeutics is a field that attracted the attention of the medical, pharmaceutical, and modeling communities during the early days of the AIDS epidemic. Its successes led to applications of modeling methods not only to HIV but a plethora of other viruses, such as hepatitis C virus (HCV), hepatitis B virus and cytomegalovirus, which along with HIV cause chronic diseases, and viruses such as influenza, respiratory syncytial virus, West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which generally cause acute infections. Here we first review the historical development of mathematical models to understand HIV and HCV infections and the effects of treatment by fitting the models to clinical data. We then focus on recent efforts and contributions of applying these models towards understanding SARS-CoV-2 infection and highlight outstanding questions where modeling can provide crucial insights and help to optimize nonpharmaceutical and pharmaceutical interventions of the coronavirus disease 2019 (COVID-19) pandemic. The review is written from our personal perspective emphasizing the power of simple target cell limited models that provided important insights and then their evolution into more complex models that captured more of the virology and immunology. To quote Albert Einstein, "Everything should be made as simple as possible, but not simpler," and this idea underlies the modeling we describe below.

Analytical Sensitivity of the Abbott BinaxNOW COVID-19 Ag Card

Multiple rapid antigen (Ag) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have recently received emergency-use authorization (EUA) from the U.S. Food and Drug Administration (FDA).

Multiple rapid antigen (Ag) tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have recently received emergency-use authorization (EUA) from the U.S. Food and Drug Administration (FDA). Although less sensitive than molecular detection methods, rapid antigen testing offers the potential for inexpensive, quick, decentralized testing. Robust analytical sensitivity data in comparison to reverse transcription-quantitative PCR (qRT-PCR) are currently lacking for many rapid antigen tests. Here, we evaluated the analytical sensitivity of the Abbott BinaxNOW COVID-19 Ag card using SARS-CoV-2-positive clinical specimens quantified by reverse transcription-droplet digital PCR (RT-ddPCR) and multiple FDA EUA qRT-PCR platforms using RNA standards. Initial and confirmatory limits of detection for the BinaxNOW COVID-19 Ag card were determined to be equivalent to 4.04 × 10⁴ to 8.06 × 10⁴ copies/swab. We further confirmed this limit of detection with 72 additional clinical samples positive for SARS-CoV-2 in either phosphate-buffered saline or viral transport medium. One hundred percent of samples with viral loads of >40,000 copies/swab were detected by rapid antigen testing. These data indicate that the BinaxNOW COVID-19 Ag card has an analytical sensitivity approximately equivalent to a generic qRT-PCR cycle threshold (C_T) value of 29 to 30.