An intra-host SARS-CoV-2 dynamics model to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation

Computer-aided drug design for virtual-screening and active-predicting of main protease (Mpro) inhibitors against SARS-CoV-2

Introduction: SARS-CoV-2 is a novel coronavirus with highly contagious and has posed a significant threat to global public health. The main protease (Mpro) is a promising target for antiviral drugs against SARS-CoV-2. Methods: In this study, we have used pharmacophore-based drug design technology to identify potential compounds from drug databases as Mpro inhibitors. Results: The procedure involves pharmacophore modeling, validation, and pharmacophore-based virtual screening, which identifies 257 compounds with promising inhibitory activity. Discussion: Molecular docking and non-bonding interactions between the targeted protein Mpro and compounds showed that ENA482732 was the best compound. These results provided a theoretical foundation for future studies of Mpro inhibitors against SARS-CoV-2.

SARS-CoV-2 Prevalence on and Incidence after Arrival in Travelers on Direct Flights from Cape Town, South Africa to Munich, Germany Shortly after Occurrence of the Omicron Variant in November/December 2021: Results from the OMTRAIR Study

The highly transmissible SARS-CoV-2-variant B.1.1.529 (Omicron) first appeared in South Africa in November 2021. In order to study Omicron entry to Germany, its occurrence related to incoming airline travel, symptomatology and compliance with entry regulations and recommendations, we conducted a cross-sectional study, followed by a retrospective cohort study among passengers and crew on 19 direct flights from Cape Town, South Africa, to Munich, Germany, between 26 November and 23 December 2021. Travelers were mandatorily PCR-tested on arrival and invited to complete an online questionnaire. SARS-CoV-2-prevalence on arrival was 3.3% (n = 90/2728), and 93% were Omicron. Of the passengers, 528 (19%) completed the questionnaire. Among participants who tested negative on arrival, self-reported SARS-CoV-2-incidence was 4.3% within 14 days, of whom 74% reported a negative PCR-test ≤ 48 h before boarding, 77% were fully vaccinated, and 90% reported wearing an FFP2/medical mask during flight. We found multiple associations between risk factors and infection on and after arrival, among which having a positive-tested travel partner was the most noteworthy. In conclusion, PCR testing before departure was insufficient to control the introduction of the Omicron variant. Additional measures (e.g., frequent testing, quarantine after arrival or travel ban) should be considered to delay virus introduction in such settings.

Analysis of continuous-time Markovian ɛ-SIS epidemics on networks

We analyze continuous-time Markovian ɛ-SIS epidemics with self-infections on the complete graph. The majority of the graphs are analytically intractable, but many physical features of the ɛ-SIS process observed in the complete graph can occur in any other graph. In this work, we illustrate that the timescales of the ɛ-SIS process are related to the eigenvalues of the tridiagonal matrix of the SIS Markov chain. We provide a detailed analysis of all eigenvalues and illustrate that the eigenvalues show staircases, which are caused by the nearly degenerate (but strictly distinct) pairs of eigenvalues. We also illustrate that the ratio between the second-largest and third-largest eigenvalue is a good indicator of metastability in the ɛ-SIS process. Additionally, we show that the epidemic threshold of the Markovian ɛ-SIS process can be accurately approximated by the effective infection rate for which the third-largest eigenvalue of the transition matrix is the smallest. Finally, we derive the exact mean-field solution for the ɛ-SIS process on the complete graph, and we show that the mean-field approximation does not correctly represent the metastable behavior of Markovian ɛ-SIS epidemics.

Replacing quarantine of COVID-19 contacts with periodic testing is also effective in mitigating the risk of transmission

The quarantine of identified close contacts has been vital to reducing transmission rates and averting secondary infection risk before symptom onset and by asymptomatic cases. The effectiveness of this contact tracing strategy to mitigate transmission is sensitive to the adherence to quarantines, which may be lower for longer quarantine periods or in vaccinated populations (where perceptions of risk are reduced). This study develops a simulation model to evaluate contact tracing strategies based on the sequential testing of identified contacts after exposure as an alternative to quarantines, in which contacts are isolated only after confirmation by a positive test. The analysis considers different number and types of tests (PCR and lateral flow antigen tests (LFA)) to identify the cost-effective testing policies that minimize the expected infecting days post-exposure considering different levels of testing capacity. This analysis suggests that even a limited number of tests can be effective at reducing secondary infection risk: two LFA tests (with optimal timing) avert infectiousness at a level that is comparable to 14-day quarantine with 80–90% adherence, or equivalently, 7–9 day quarantine with full adherence (depending on the sensitivity of the LFA test). Adding a third test (PCR or LFA) reaches the efficiency of a 14-day quarantine with 90–100% adherence. These results are robust to the exposure dates of the contact, test sensitivity of LFA and alternative models of viral load evolution, which suggests that simple testing rules can be effective for improving contact tracing in settings where strict quarantine adherence is difficult to implement.

Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States

Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number ℛ0, the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of ℛ0 relates to a herd immunity threshold (HIT), which is given by 1-1/ℛ0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level ℛ0 estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. ℛ0 estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21 January 2020 to 21 June 2020. Our ℛ0 estimates characterize the infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we found that no state had achieved herd immunity as of 20 September 2021.

Diagnostic Accuracy of SARS-CoV-2 Antigen Tests for Community Transmission Screening: A Systematic Review and Meta-Analysis

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) caused the global pandemic of coronavirus disease 2019 (COVID-19). Rapid identification and isolation of infectious patients are critical methods to block COVID-19 transmission. Antigen tests can contribute to prompt identification of infectious individuals. This meta-analysis aims to evaluate the diagnostic accuracy of antigen tests for SARS-CoV-2. We conducted a literature search in PubMed, Embase, the Cochrane Library, and Biomed Central databases. Studies evaluating the diagnostic accuracy of antigen tests for SARS-CoV-2 in community participants were included. Only English-language articles were reviewed. We included eligible studies that provided available data to construct a 2 × 2 table on a per-patient basis. Overall sensitivity and specificity for antigen tests were generated using a bivariate random-effects model. Eighteen studies with 34,865 participants were retrieved. The meta-analysis for SARS-CoV-2 antigen tests generated a pooled sensitivity of 0.82 and a pooled specificity of 1.00. A subgroup analysis of ten studies that reported outcomes for 5629 symptomatic participants generated a pooled sensitivity of 0.87 and a pooled specificity of 1.00. Antigen tests might have higher sensitivity in detecting SARS-CoV-2 in symptomatic patients in the community and may be an effective tool to identify patients to be quarantined to prevent further SARS-CoV-2 transmission.

Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020

By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe against simulated outbreaks and elaborate phylodynamic analyses. Using available sequence data, we reconstruct incidence histories for Denmark, Scotland, Switzerland, and Victoria (Australia) and demonstrate, how to use the method to investigate the effects of changing testing policies on case ascertainment. Specifically, we find that under-reporting was highest during summer 2020 in Europe, coinciding with more liberal testing policies at times of low testing capacities. Due to the increased use of real-time sequencing, it is envisaged that GInPipe can complement established surveillance tools to monitor the SARS-CoV-2 pandemic. In post-pandemic times, when diagnostic efforts are decreasing, GInPipe may facilitate the detection of hidden infection dynamics.

[SARS-CoV-2 transmission routes and implications for self- and non-self-protection]

Die weltweite Ausbreitung des Coronavirus SARS-CoV‑2 hat Gesundheits‑, Wirtschafts- und Gesellschaftssysteme massiv in Mitleidenschaft gezogen. Obwohl mittlerweile effektive Impfstoffe zur Verfügung stehen, ist es wahrscheinlich, dass der Erreger endemisch wird und uns noch über Jahre begleitet. Um andere und sich selbst möglichst effektiv vor einer SARS-CoV-2-Infektion zu schützen, ist ein Verständnis der Übertragungswege von größter Wichtigkeit.

In dieser Übersichtsarbeit erläutern wir Übertragungswege im Hinblick auf den Fremd- und Eigenschutz. Darüber hinaus gehen wir auf die Charakteristika der SARS-CoV-2-Übertragung auf Populationsebene ein. Diese Arbeit soll helfen, folgende Fragen anhand der verfügbaren Literatur zu beantworten: Wann und wie lange ist eine infizierte Person kontagiös (ansteckungsfähig)? Wie wird das Virus ausgeschieden? Wie wird das Virus aufgenommen? Wie verbreitet sich das Virus in der Gesellschaft?

Die Mensch-zu-Mensch-Übertragung von SARS-CoV‑2 wird in starkem Maße durch die biologischen Erregereigenschaften, einschließlich der Infektions‑, Replikations- und Ausscheidungskinetik, bestimmt. SARS-CoV‑2 wird hauptsächlich über humane Aerosole übertragen, die von infizierten Personen ausgeschieden werden, auch wenn Erkrankungssymptome (noch) nicht vorliegen. Hieraus resultiert ein relevanter Anteil prä- bzw. asymptomatischer Transmissionen. In geschlossenen Räumen erfolgen Übertragungen besonders effektiv. Die meisten infizierten Personen rufen eine geringe Zahl von Sekundärfällen hervor, während wenige Fälle (sog. Superspreader) zu vielen Folgeinfektionen führen – auf Populationsebene spricht man hier von einer „Überdispersion“. Die besonderen Merkmale von SARS-CoV‑2 (asymptomatische Aerosolübertragung und Überdispersion) machen die Pandemie schwer kontrollierbar.

Trends in respiratory virus circulation following COVID-19-targeted nonpharmaceutical interventions in Germany, January - September 2020: Analysis of national surveillance data

BACKGROUND

During the initial COVID-19 response, Germany's Federal Government implemented several nonpharmaceutical interventions (NPIs) that were instrumental in suppressing early exponential spread of SARS-CoV-2. NPI effect on the transmission of other respiratory viruses has not been examined at the national level thus far.

METHODS

Upper respiratory tract specimens from 3580 patients with acute respiratory infection (ARI), collected within the nationwide German ARI Sentinel, underwent RT-PCR diagnostics for multiple respiratory viruses. The observation period (weeks 1-38 of 2020) included the time before, during and after a far-reaching contact ban. Detection rates for different viruses were compared to 2017-2019 sentinel data (15350 samples; week 1-38, 11823 samples).

FINDINGS

The March 2020 contact ban, which was followed by a mask mandate, was associated with an unprecedented and sustained decline of multiple respiratory viruses. Among these, rhinovirus was the single agent that resurged to levels equalling those of previous years. Rhinovirus rebound was first observed in children, after schools and daycares had reopened. By contrast, other nonenveloped viruses (i.e. gastroenteritis viruses reported at the national level) suppressed after the shutdown did not rebound.

INTERPRETATION

Contact restrictions with a subsequent mask mandate in spring may substantially reduce respiratory virus circulation. This reduction appears sustained for most viruses, indicating that the activity of influenza and other respiratory viruses during the subsequent winter season might be low,whereas rhinovirus resurgence, potentially driven by transmission in educational institutions in a setting of waning population immunity, might signal predominance of rhinovirus-related ARIs.

FUNDING

Robert Koch-Institute and German Ministry of Health.

COVIDStrategyCalculator: A software to assess testing and quarantine strategies for incoming travelers, contact management, and de-isolation

While large-scale vaccination campaigns against SARS-CoV-2 are rolled out at the time of writing, non-pharmaceutical interventions (NPIs), including the isolation of infected individuals and quarantine of exposed individuals, remain central measures to contain the spread of SARS-CoV-2. Strategies that combine NPIs with innovative SARS-CoV-2 testing strategies may increase containment efficacy and help to shorten quarantine durations. We developed a user-friendly software tool that implements a recently published stochastic within-host viral dynamics model that captures temporal attributes of the viral infection, such as test sensitivity, infectiousness, and the occurrence of symptoms. Based on this model, the software allows to evaluate the efficacy of user-defined, arbitrary NPI and testing strategies in reducing the transmission potential in different contexts. The software thus enables decision makers to explore NPI strategies and perform hypothesis testing, e.g., with regard to the utilization of novel diagnostics or with regard to containing novel virus variants.