### Overview

MeSH Disease

Disease (94)

Infections (82)

Death (26)

Pneumonia (16)

Human Phenotype

Pneumonia (17)

Fever (9)

Falls (9)

Cough (5)

Sneeze (2)

Transmission

Seroprevalence
displaying 1 - 10 records in total 181
records per page

### Household Representative Sample Strategy for COVID-19 Large-Scale Population Screening

Authors: John Takyi-Williams

id:10.20944/preprints202008.0030.v1 Date: 2020-08-02 Source: Preprints.org

In the advent of COVID-19 pandemic, testing is highly essential to be able to isolate, treat infected persons, and finally curb transmission TRANS of this infectious respiratory disease MESHD. Group testing has been used previously for various infectious diseases MESHD and recently reported for large-scale population testing of COVID-19. However, possible sample dilution as a result of large pool sizes has been reported, limiting testing methods’ detection sensitivity SERO. Moreover, the need to sample all individuals prior to pooling overburden the limited resources such as test kits. An alternative proposed strategy where test is performed on pooled samples from individuals representing different households is presented here. This strategy intends to improve group testing method through the reduction in the number of samples collected and pooled during large-scale population testing. Moreover, it introduces database system which enables continuous monitoring of the population’s virus exposure for better decision making.

### Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19.

Authors: Giselle Ibette Silva Lopez-Lopes; Cintia Mayumi Ahagon; Margarete Aparecida Bonega; Fabiana Pereira dos Santos; Katia Correa de Oliveira Santos; Audrey Cilli; Lincoln Spinazola do Prado; Daniela Bernardes Borges da Silva; Nuria Borges da Luz; Claudia Patara Saraceni; Ana Maria Sardinha Afonso; Maria do Carmo Timenetsky; Luis Fernando de Macedo Brigido

doi:10.1101/2020.07.29.20163998 Date: 2020-08-01 Source: medRxiv

Background: SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection MESHD. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance SERO of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute. Methods: Consecutive volunteer testing of LWH and external household and close contacts TRANS were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea). Results: Four hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection MESHD observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease MESHD. Over a third (38%) of asymptomatic TRANS cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic TRANS and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease TRANS disease MESHD.

### Hybrid capture-based sequencing enables unbiased recovery of SAR TRANS-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants

Authors: Mingkun Li; Yi Xu; Lu Kang; Zijie Shen; Xufang Li; Weili Wu; Wentai Ma; Chunxiao Fang; Fengxia Yang; Xuan Jiang; Sitang Gong; Li Zhang

doi:10.1101/2020.07.30.230102 Date: 2020-08-01 Source: bioRxiv

Background: In response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission TRANS, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples. Methods: Eighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization. Results: By examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance SERO of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period. Conclusions: The hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.

### Incidence and outcomes of healthcare-associated COVID-19 infections MESHD: significance of delayed diagnosis and correlation with staff absence

Authors: Kirstin Khonyongwa; Surabhi K Taori; Ana Soares; Nergish Desai; Malur Sudhanva; William Bernal; Silke Schelenz; Lisa A Curran

doi:10.1101/2020.07.24.20148262 Date: 2020-07-30 Source: medRxiv

Background: The sudden increase in COVID-19 admissions in hospitals during the SARS-CoV2 pandemic of 2020 has led to onward transmissions TRANS among vulnerable inpatients. Aims: This study was performed to evaluate the prevalence SERO and clinical outcomes of Healthcare-associated COVID-19 infections MESHD (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission TRANS in a London Teaching Hospital Trust. Methods: Electronic laboratory, patient and staff self-reported sickness records were interrogated for the period 1st March to 18th April 2020. HA-COVID-19 was defined as symptom onset TRANS >14d of admission. Test performance SERO of a single combined throat and nose swab (CTNS) for patient placement and the effect of delayed RNA positivity (DRP, defined as >48h delay) on patient outcomes was evaluated. The incidence of staff self-reported COVID-19 sickness absence, hospital bed occupancy, community incidence and DRP was compared HA-COVID-19. The incidence of other significant hospital-acquired bacterial infections MESHD (OHAI) was compared to previous years. Results: 58 HA-COVID-19 (7.1%) cases were identified. As compared to community-acquired cases, significant differences were observed in age TRANS (p=0.018), ethnicity (p<0.001) and comorbidity burden (p<0.001) but not in 30d mortality. CTNS negative predictive value SERO was 60.3%. DRP was associated with greater mortality (p=0.034) and 34.5% HA-COVID-19 cases could be traced TRANS to delayed diagnosis in CA-COVID-19. Incidence of HA-COVID-19 correlated positively with DRP (R=0.7108) and staff sickness absence (R=0.7815). OHAI rates were similar to previous 2 years. Conclusion: Early diagnosis and isolation of COVID-19 would help reduce transmission TRANS. A single CTNS has limited value in segregating patients into positive and negative pathways.

### SARS-CoV-2 antibody SERO responses determine disease MESHD severity in COVID-19 infected individuals

Authors: Cecilie Bo Hansen; Ida Jarlhelt; Laura Pérez-Alós; Lone Hummelshøj Landsy; Mette Loftager; Anne Rosbjerg; Charlotte Helgstrand; Jais Rose Bjelke; Thomas Egebjerg; Joseph G. Jardine; Charlotte Sværke Jørgensen; Kasper Iversen; Rafael Bayarri-Olmos; Peter Garred; Mikkel-Ole Skjoedt

doi:10.1101/2020.07.27.20162321 Date: 2020-07-29 Source: medRxiv

Globally, the COVID-19 pandemic has had extreme consequences for the healthcare system and calls for diagnostic tools to monitor and understand the transmission TRANS, pathogenesis and epidemiology, as well as to evaluate future vaccination strategies. Here we have developed novel flexible ELISA SERO-based assays for specific detection of SARS-CoV-2 antibodies SERO against the receptor-binding domain (RBD): An antigen sandwich- ELISA SERO relevant for large population screening and three isotype-specific assays for in-depth diagnostics. Their performance SERO was evaluated in a cohort of 350 convalescent participants with previous COVID-19 infection MESHD, ranging from asymptomatic TRANS to critical cases. We mapped the antibody SERO responses to different areas on protein N and S and showed that the IgM, A and G antibody SERO responses against RBD are significantly correlated to the disease MESHD severity. These assays-and the data generated from them-are highly relevant for diagnostics and prognostics and contribute to the understanding of long-term COVID-19 immunity.

### Test for Covid-19 seasonality and the risk of second waves

Authors: Francois A. Engelbrecht; Robert J. Scholes

doi:10.21203/rs.3.rs-50313/v1 Date: 2020-07-28 Source: ResearchSquare

Eight months into the Covid-19 pandemic it remains unclear whether transmission TRANS of SARS-CoV-2 is affected by climate factors. Using a dynamic epidemiological model with Covid-19 climate sensitivity SERO in the likely range, we demonstrate why attempts to detect a climate signal in Covid-19 have thus far been inconclusive. Then we formulate a novel methodology and related criteria that can be used to test for seasonal climate sensitivity SERO in observed Covid-19 infection MESHD data. We show that if the disease MESHD does have a substantial seasonal dependence, and herd immunity is not established during the first peak season of the outbreak (or a vaccine does not become available), there is likely to be a seasonality-sensitive second wave of infections MESHD about one year after the initial outbreak. In regions where non-pharmaceutical control has contained the disease MESHD in the first year of outbreak and thus kept a large portion of the population susceptible, the second wave may be substantially larger in amplitude than the first if control measures are relaxed. This is simply because it develops under the favorable conditions of a full autumn to winter period and from a larger pool of infected individuals.

### The performance SERO of Mobile Cabin Hospital in combatting COVID-19 in China

Authors: Hongru Li; Jiaping Lin II; Hongmei Lian; Kang Chen; Yongtao Lyu; Yusheng Chen; Lili Ren; Li Zheng; Zhisheng Lin; Xueying Yu; Zihan Chen; Christopher Rensing; Xin Qian; Xinghai Yang

doi:10.1101/2020.07.26.20162206 Date: 2020-07-28 Source: medRxiv

Background: Since the end of 2019 to the present day, the outbreak of the coronavirus disease MESHD 2019 (COVID-19) has had an immense impact on China and on other countries worldwide. This outbreak represents a serious threat to the lives and health of people all around the world. The epidemic first broke out in Wuhan, where the Chinese government was unable to prevent the spread of the disease TRANS disease MESHD by implementing home quarantine measures. Mobile cabin hospitals were used to relieve pressure on hospitals due to the need for beds while also isolating the sources of the infection MESHD through a centralized quarantine and treatment of mild cases. Method: This paper reviewed and summarized the treatment of patients with mild illness and symptoms during the period from the construction to the closing of the Hanyang Mobile Cabin Hospital in Wuhan, China, and presented the operational elements and possible improvements of running this hospital. Results: Mobile cabin hospitals helped China to curb the epidemic in only 2 incubation periods TRANS in 28 days.The basic conditions required for a normal operation of mobile cabin hospitals included the selection of the environment, medical staff to patient ratio, organizational structure, management model, admission criteria, treatment approaches, discharge process, livelihood guarantee, security, and other safeguarding measures. All of these components were performed carefully in Wuhan Hanyang Mobile Cabin Hospital, without medical staff being infected. Conclusion: The mobile cabin hospital compulsory quarantine for mild patients was an alternative method to combat COVID-19. It is hoped that the presented work in this manuscript can serve as a reference for the emergency MESHD prevention and control measures for global epidemic outbreaks.

### Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

Authors: Ozlem Akgun Dogan; Betsi Kose; Nihat Bugra Agaoglu; Jale Yildiz; Gizem Alkurt; Yasemin Kendir Demirkol; Arzu Irvem; Gizem Dinler-Doganay; Levent Doganay

doi:10.1101/2020.07.26.20158618 Date: 2020-07-28 Source: medRxiv

The gold standard method in the diagnosis of SARS-CoV-2 infection MESHD is the detection of viral RNA in nasopharyngeal sample by RT-PCR. Recently, saliva samples has been suggested as an alternative due to being fast, reliable and non-invasive, rather than nasopharyngeal samples. We compared RT-PCR results in nasopharyngeal, oro-nasopharyngeal and saliva samples of COVID-19 patients. 98 of 200 patients were positive in RT-PCR analysis performed before the hospitalization. In day 0, at least one sample was positive in 67% of 98 patients. Positivity rate was 83% for both oro-nasopharyngeal and nasopharyngeal samples, while it was 63% for saliva samples (p<0.001). On day 5, RT-PCR was performed in 59 patients, 34% had at least one positive result. The positivity rate was 55% for saliva and nasopharyngeal samples, while it was 60% for oro-nasopharyngeal samples. Our study shows that the sampling saliva does not increase the sensitivity SERO of RT-PCR tests at early stages of infection MESHD. However, on 5th day, viral RNA detection rates in saliva were similar to nasopharyngeal and oro-nasopharyngeal samples. In conclusion, we suggest that, in patients receiving treatment, virus presence in saliva, in addition to the standard samples, is important to determine the isolation period and to control the transmission TRANS.

### On the robustness of effectiveness estimation of nonpharmaceutical interventions against COVID-19 transmission TRANS

Authors: Mrinank Sharma; Sören Mindermann; Jan Markus Brauner; Gavin Leech; Anna B. Stephenson; Tomáš Gavenčiak; Jan Kulveit; Yee Whye Teh; Leonid Chindelevitch; Yarin Gal

id:2007.13454v1 Date: 2020-07-27 Source: arXiv

There remains much uncertainty about the relative effectiveness of different nonpharmaceutical interventions (NPIs) against COVID-19 transmission TRANS. Several studies attempt to infer NPI effectiveness with cross-country, data-driven modelling, by linking from NPI implementation dates to the observed timeline of cases and deaths MESHD in a country. These models make many assumptions. Previous work sometimes tests the sensitivity SERO to variations in explicit epidemiological model parameters, but rarely analyses the sensitivity SERO to the assumptions that are made by the choice the of model structure (structural sensitivity SERO analysis). Such analysis would ensure that the inferences made are consistent under plausible alternative assumptions. Without it, NPI effectiveness estimates cannot be used to guide policy. We investigate four model structures similar to a recent state-of-the-art Bayesian hierarchical model. We find that the models differ considerably in the robustness of their NPI effectiveness estimates to changes in epidemiological parameters and the data. Considering only the models that have good robustness, we find that results and policy-relevant conclusions are remarkably consistent across the structurally different models. We further investigate the common assumptions that the effect of an NPI is independent of the country, the time, and other active NPIs. We mathematically show how to interpret effectiveness estimates when these assumptions are violated.

### Analyzing the dominant SARS-CoV-2 transmission TRANS modes towards an ab-initio SEIR model

Authors: Swetaprovo Chaudhuri; Saptarshi Basu; Abhishek Saha

id:2007.13596v1 Date: 2020-07-27 Source: arXiv

In this work, different transmission TRANS modes of the SARS-CoV-2 virus and their role in determining the evolution of the Covid-19 pandemic are analyzed. Probability of infection MESHD caused by inhaling infectious droplets (initial, ejection diameters between 0.5-750$\mu m$) and probability of infection MESHD by the corresponding desiccated nuclei that mostly encapsulate the virions post droplet evaporation, are calculated. At typical, air-conditioned yet quiescent, large indoor space, for the average viral loading, and at early times, cough MESHD cough HP droplets of initial diameter between $10 \mu m$ and $50 \mu m$ have the highest infection MESHD probability. However, by the time they are to be inhaled, the diameters are most likely $5-6$ times smaller with respect to their initial diameters. While the initially near unity infection MESHD probability due to droplets (airborne/ballistic) rapidly decays within the first $25$s, the small yet persistent infection MESHD probability of airborne desiccated nuclei decays appreciably only by $1000$s. Combined with molecular collision theory adapted to calculate frequency of contact TRANS frequency of contact SERO between the susceptible population and the droplet/nuclei cloud, infection MESHD probabilities are used to define infection MESHD rate constants, ab-initio, leading to a SEIR model. Assuming the virus sustains equally well within the dried droplet nuclei as in the droplets, the floating nuclei leads to a stronger contribution to the corresponding rate constants with respect to the droplets, in the above-mentioned conditions. Combining both pathways, the basic reproduction number TRANS $\mathcal{R}_0$ caused by cough MESHD cough HP droplets and nuclei are calculated. Viral load, minimum infectious dose, sensitivity SERO of the virus half-life to the phase of its vector, extent of dilution of the respiratory jet/puff by the entraining air are the important factors that determine specific physical modes of transmission TRANS and the pandemic evolution.

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 All MeSH Disease Human Phenotype Transmission Seroprevalence

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