Modeling the effectiveness of olfactory testing to limit SARS-CoV-2 transmission

Modeling the transmission mitigation impact of testing for infectious diseases

A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus but delayed by up to two days to control omicron-era severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, while rapid tests are superior to reverse transcription quantitative polymerase chain reaction (RT-qPCR) to control founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Last, we illustrate the model's flexibility by quantifying trade-offs in the use of post-diagnosis testing to shorten isolation times.

Economic Evaluation of COVID-19 Screening Tests and Surveillance Strategies in Low-Income, Middle-Income, and High-Income Countries: A Systematic Review

BACKGROUND Economic evaluation of the testing strategies to control transmission and monitor the severity of COVID-19 after the pandemic is essential. This study aimed to review the economic evaluation of COVID-19 tests and to construct a model with outcomes in terms of cost and test acceptability for surveillance in the post-pandemic period in low-income, middle-income, and high-income countries. MATERIAL AND METHODS We performed the systematic review following PRISMA guidelines through MEDLINE and EMBASE databases. We included the relevant studies that reported the economic evaluation of COVID-19 tests for surveillance. Also, we input current probability, sensitivity, and specificity for COVID-19 surveillance in the post-pandemic period. RESULTS A total of 104 articles met the eligibility criteria, and 8 articles were reviewed and assessed for quality. The specificity and sensitivity of COVID-19 screening tests were reported as 80% to 90% and 40% to 90%, respectively. The target population presented a mortality rate between 0.2% and 19.2% in the post-pandemic period. The implementation model of COVID-19 screening tests for surveillance with a cost mean for molecular and antigen tests was US$ 46.64 (min-max US $0.25-$105.39) and US $6.15 (min-max US $2-$10), respectively. CONCLUSIONS For the allocation budget for the COVID-19 surveillance test, it is essential to consider the incidence and mortality of the post-pandemic period in low-income, middle-income, and high-income countries. A robust method to evaluate outcomes is needed to prevent increasing COVID-19 incidents earlier.

Modeling the Transmission Mitigation Impact of Testing for Infectious Diseases

A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)-the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale-and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today's rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus (RSV), but delayed by up to 2d to control omicron-era SARS-CoV-2. Furthermore, while rapid tests are superior to RT-qPCR for control of founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Finally, we illustrate the model's flexibility by quantifying tradeoffs in the use of post-diagnosis testing to shorten isolation times.

Analysis of the risk and pre-emptive control of viral outbreaks accounting for within-host dynamics: SARS-CoV-2 as a case study

In the era of living with COVID-19, the risk of localised SARS-CoV-2 outbreaks remains. Here, we develop a multiscale modelling framework for estimating the local outbreak risk for a viral disease (the probability that a major outbreak results from a single case introduced into the population), accounting for within-host viral dynamics. Compared to population-level models previously used to estimate outbreak risks, our approach enables more detailed analysis of how the risk can be mitigated through pre-emptive interventions such as antigen testing. Considering SARS-CoV-2 as a case study, we quantify the within-host dynamics using data from individuals with omicron variant infections. We demonstrate that regular antigen testing reduces, but may not eliminate, the outbreak risk, depending on characteristics of local transmission. In our baseline analysis, daily antigen testing reduces the outbreak risk by 45% compared to a scenario without antigen testing. Additionally, we show that accounting for heterogeneity in within-host dynamics between individuals affects outbreak risk estimates and assessments of the impact of antigen testing. Our results therefore highlight important factors to consider when using multiscale models to design pre-emptive interventions against SARS-CoV-2 and other viruses.

Computer-aided drug design combined network pharmacology to explore anti-SARS-CoV-2 or anti-inflammatory targets and mechanisms of Qingfei Paidu Decoction for COVID-19

Introduction

Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. Severe cases of COVID-19 are characterized by an intense inflammatory process that may ultimately lead to organ failure and patient death. Qingfei Paidu Decoction (QFPD), a traditional Chines e medicine (TCM) formula, is widely used in China as anti-SARS-CoV-2 and anti-inflammatory. However, the potential targets and mechanisms for QFPD to exert anti-SARS-CoV-2 or anti-inflammatory effects remain unclear.

Methods

In this study, Computer-Aided Drug Design was performed to identify the antiviral or anti-inflammatory components in QFPD and their targets using Discovery Studio 2020 software. We then investigated the mechanisms associated with QFPD for treating COVID-19 with the help of multiple network pharmacology approaches.

Results and discussion

By overlapping the targets of QFPD and COVID-19, we discovered 8 common targets (RBP4, IL1RN, TTR, FYN, SFTPD, TP53, SRPK1, and AKT1) of 62 active components in QFPD. These may represent potential targets for QFPD to exert anti-SARS-CoV-2 or anti-inflammatory effects. The result showed that QFPD might have therapeutic effects on COVID-19 by regulating viral infection, immune and inflammation-related pathways. Our work will promote the development of new drugs for COVID-19.

Olfactory testing as COVID-19 screening in school children; A prospective cross-sectional study

BACKGROUND

Little is known about olfactory changes in pediatric COVID-19. It is possible that children under-report chemosensory changes on questionnaires, similar to reports in adults. Here, we aim to describe COVID-19-related olfactory dysfunction in outpatient children. We hypothesized that children with COVID-19 will demonstrate abnormal olfaction on smell-identification testing at a higher rate than children with negative COVID-19 testing.

METHODS

A prospective cross-sectional study was undertaken from June 2020-June 2021 at a tertiary care pediatric hospital. A consecutive sample of 205 outpatients aged 5-21 years undergoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) PCR testing were approached for this study. Patients with prior olfactory dysfunction were excluded. Participants were given a standard COVID-19 symptom questionnaire, a Smell Identification Test (SIT) and home-odorant-based testing within 2 weeks of COVID-19 testing. Prior to study enrollment, power calculation estimated 42 patients to determine difference in rates of SIT results between groups. Data were summarized with descriptive statistics.

RESULTS

Fifty-one patients underwent smell identification testing (23 positive (45%) and 28 negative (55%) for COVID-19; mean age 12.7 years; 60% female). 92% of all patients denied subjective change in their sense of smell or taste but only 58.8% were normosmic on testing. There was no difference in screening questionnaires or SIT scores between COVID-19 positive and negative groups.

CONCLUSIONS

Unlike adults, there was no statistical difference in olfactory function between outpatient COVID-19 positive and negative children. Our findings suggest a discrepancy between objective and patient-reported olfactory function in pediatric patients, and poor performance of current screening protocols at detecting pediatric COVID-19.

SARS-CoV-2 transmission and impacts of unvaccinated-only screening in populations of mixed vaccination status

Screening programs that test only the unvaccinated population have been proposed and implemented to mitigate SARS-CoV-2 spread, implicitly assuming that the unvaccinated population drives transmission. To evaluate this premise and quantify the impact of unvaccinated-only screening programs, we introduce a model for SARS-CoV-2 transmission through which we explore a range of transmission rates, vaccine effectiveness scenarios, rates of prior infection, and screening programs. We find that, as vaccination rates increase, the proportion of transmission driven by the unvaccinated population decreases, such that most community spread is driven by vaccine-breakthrough infections once vaccine coverage exceeds 55% (omicron) or 80% (delta), points which shift lower as vaccine effectiveness wanes. Thus, we show that as vaccination rates increase, the transmission reductions associated with unvaccinated-only screening decline, identifying three distinct categories of impact on infections and hospitalizations. More broadly, these results demonstrate that effective unvaccinated-only screening depends on population immunity, vaccination rates, and variant.

Olfactory Dysfunction in Patients With Coronavirus Disease 2019: A Review

The coronavirus disease 2019 (COVID-19) pandemic is wreaking havoc on public-health and economic systems worldwide. Among the several neurological symptoms of patients with COVID-19 reported in clinical practice, olfactory dysfunction (OD) is the most common. OD occurs as the earliest or the only clinical manifestation in some patients. Increasing research attention has focused on OD, which is listed as one of the main diagnostic symptoms of severe acute respiratory syndrome-coronavirus-2 infection. Multiple clinical and basic-science studies on COVID-19-induced OD are underway to clarify the underlying mechanism of action. In this review, we summarize the clinical characteristics, mechanisms, evaluation methods, prognosis, and treatment options of COVID-19-induced OD. In this way, we hope to improve the understanding of COVID-19-induced OD to aid early identification and precise intervention.

Screening of COVID-19 cases through a Bayesian network symptoms model and psychophysical olfactory test

The sudden loss of smell is among the earliest and most prevalent symptoms of COVID-19 when measured with a clinical psychophysical test. Research has shown the potential impact of frequent screening for olfactory dysfunction, but existing tests are expensive and time consuming. We developed a low-cost ($0.50/test) rapid psychophysical olfactory test (KOR) for frequent testing and a model-based COVID-19 screening framework using a Bayes Network symptoms model. We trained and validated the model on two samples: suspected COVID-19 cases in five healthcare centers (n = 926; 33% prevalence, 309 RT-PCR confirmed) and healthy miners (n = 1,365; 1.1% prevalence, 15 RT-PCR confirmed). The model predicted COVID-19 status with 76% and 96% accuracy in the healthcare and miners samples, respectively (healthcare: AUC = 0.79 [0.75-0.82], sensitivity: 59%, specificity: 87%; miners: AUC = 0.71 [0.63-0.79], sensitivity: 40%, specificity: 97%, at 0.50 infection probability threshold). Our results highlight the potential for low-cost, frequent, accessible, routine COVID-19 testing to support society's reopening.

Massively collaborative crowdsourced research on COVID19 and the chemical senses: Insights and outcomes

In March 2020, the Global Consortium of Chemosensory Research (GCCR) was founded by chemosensory researchers to address emerging reports of unusual smell and taste dysfunction arising from the SARS-CoV-2 pandemic. Over the next year, the GCCR used a highly collaborative model, along with contemporary Open Science practices, to produce multiple high impact publications on chemosensation and COVID19. This invited manuscript describes the founding of the GCCR, the tools and approaches it used, and a summary of findings to date. These findings are contextualized within a summary of some of the broader insights about chemosensation (smell, taste, and chemesthesis) and COVID19 gained over the last 18 months, including potential mechanisms of loss. Also, it includes a detailed discussion of some current Open Science approaches and practices used by the GCCR to increase transparency, rigor, and reproducibility.

Higher viral load drives infrequent SARS-CoV-2 transmission between asymptomatic residence hall roommates

BACKGROUND

The COVID-19 pandemic spread to over 200 countries in less than six months. To understand COVID spread, determining transmission rate and defining factors that increase transmission risk are essential. Most cases are asymptomatic, but they have viral loads indistinguishable from symptomatic people and do transmit SARS-CoV-2 virus. However, they are often undetected.

METHODS

Given high residence hall student density, the University of Colorado Boulder established a mandatory weekly screening test program. We analyzed longitudinal data of 6408 students and identified 116 likely transmission events in which a second roommate tested positive within 14 days of the index roommate.

RESULTS

Although the infection rate was lower in single rooms (10%) than in multiple-occupancy rooms (19%), inter-roommate transmission only occurred ~20% of the time. Cases were usually asymptomatic at the time of detection. Notably, individuals who likely transmitted had an average viral load ~6.5-fold higher than individuals who did not (mean Cq 26.2 vs 28.9). Although diagnosed students moved to isolation rooms, there was no difference in time-to-isolation between cases with or without inter-roommate transmission.

CONCLUSIONS

This analysis argues that inter-roommate transmission occurs infrequently in residence halls and provides strong correlative evidence that viral load is proportional to transmission probability.