Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (71)

Fever (54)

Cough (50)

Falls (22)

Fatigue (16)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 1167
    records per page




    Extended lifetime of respiratory droplets in a turbulent vapour puff and its implications on airborne disease MESHD transmission TRANS

    Authors: Kai Leong Chong; Chong Shen Ng; Naoki Hori; Rui Yang; Roberto Verzicco; Detlef Lohse

    doi:10.1101/2020.08.04.20168468 Date: 2020-08-06 Source: medRxiv

    To mitigate the COVID-19 pandemic, it is key to slow down the spreading of the life-threatening coronavirus (SARS-CoV-2). This spreading mainly occurs through virus-laden droplets expelled at speaking, screaming, shouting, singing, coughing MESHD coughing HP, sneezing MESHD sneezing HP, or even breathing [1-7]. To reduce infections MESHD through such respiratory droplets, authorities all over the world have introduced the so-called "2-meter distance rule" or "6-foot rule". However, there is increasing empirical evidence, e.g. through the analysis of super-spreading events [6, 8-11], that airborne transmission TRANS of the coronavirus over much larger distances plays a major role [1-3, 7, 12-15], with tremendous implications for the risk assessment of coronavirus transmission TRANS. It is key to better and fundamentally understand the environmental ambient conditions under which airborne transmission TRANS of the coronavirus is likely to occur, in order to be able to control and adapt them. Here we employ direct numerical simulations of a typical respiratory aerosol in a turbulent jet of the respiratory event within a Lagrangian-Eulerian approach [16-18] with 5000 droplets, coupled to the ambient velocity, temperature, and humidity fields to allow for exchange of mass and heat [19] and to realistically account for the droplet evaporation under different ambient conditions. We found that for an ambient relative humidity of 50% the lifetime of the smallest droplets of our study with initial diameter of 10 m gets extended by a factor of more than 30 as compared to what is suggested by the classical picture of Wells [20, 21], due to collective effects during droplet evaporation and the role of the respiratory humidity [22], while the larger droplets basically behave ballistically. With increasing ambient relative humidity the extension of the lifetimes of the small droplets further increases and goes up to 150 times for 90% relative humidity, implying more than two meters advection range of the respiratory droplets within one second. Smaller droplets live even longer and travel TRANS further. Our results may explain why COVID-19 superspreading events can occur for large ambient relative humidity such as in cooled-down meat-processing plants [10] or in pubs with poor ventilation. We anticipate our tool and approach to be starting points for larger parameter studies and for optimizing ventilation and indoor humidity controlling concepts, which in the upcoming autumn and winter both will be key in mitigating the COVID-19 pandemic.

    Genomic epidemiology reveals transmission TRANS patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

    Authors: Jemma L Geoghegan; Xiaoyun Ren; Matthew Storey; James Hadfield; Lauren Jelley; Sarah Jefferies; Jill Sherwood; Shevaun Paine; Sue Huang; Jordan Douglas; Fabio K L Mendes; Andrew Sporle; Michael G Baker; David R Murdoch; Nigel French; Colin R Simpson; David Welch; Alexei J Drummond; Edward C Holmes; Sebastian Duchene; Joep de Ligt

    doi:10.1101/2020.08.05.20168930 Date: 2020-08-06 Source: medRxiv

    New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand has now effectively eliminated the virus, with low numbers of new cases limited to new arrivals in managed quarantine facilities at the border. Here, we generated 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected between 26 February and 22 May 2020, representing 56% of all confirmed cases TRANS in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number TRANS, Re, of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission TRANS lineage of more than one additional case. Most of the cases that resulted in a transmission TRANS lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections MESHD to a major transmission TRANS cluster than through epidemiological data alone, providing probable sources of infections MESHD for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease MESHD mitigation.

    Early transmission TRANS dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama.

    Authors: Danilo Franco; Claudia Gonzalez; Leyda E Abrego; Jean P Carrera; Yamilka Diaz; Yaset Caisedo; Ambar Moreno; Oris Chavarria; Jessica Gondola; Marlene Castillo; Elimelec Valdespino; Melissa Gaitan; Jose Martinez-Mandiche; Lizbeth Hayer; Pablo Gonzalez; Carmen Lange; Yadira Molto; Dalis Mojica; Ruben Ramos; Maria Mastelari; Lizbeth Cerezo; Lourdes Moreno; Christl A Donnelly; Nuno R. Faria; Juan M Pascale; Sandra Lopez-Verges; Alexander A Martinez

    doi:10.1101/2020.07.31.20160929 Date: 2020-08-04 Source: medRxiv

    Background With more than 50000 accumulated cases, Panama has one of the highest incidences of SARS-CoV-2 in Central America, despite the fast implementation of disease MESHD control strategies. We investigated the early transmission TRANS patterns of the virus and the outcomes of mitigation measures in the country. Methods We collected information from epidemiological surveillance, including contact tracing TRANS, and genetic data from SARS-CoV-2 whole genomes, of the first five weeks of the outbreak. These data were used to estimate the exponential growth rate, doubling time and the time-varying effective reproductive number TRANS (Rt) using date of symptom onset TRANS in a Bayesian framework. The time of most recent ancestor for the introduced and circulating lineages was estimated by Bayesian analysis. Findings A total of 4210 subjects were SARS-CoV-2 positive during the period evaluated, of them we sequenced 313 cases, detecting the circulation of 10 SARS-CoV-2 lineages. Whole genomes analysis identified the local transmission TRANS of one cryptic lineage as early as 2 weeks before it was detected by surveillance systems. Analysis of transmission TRANS dynamics showed that lockdown reduced Rt and increased the doubling time, however, these measures did not stop the circulation of this lineage in the country. Interpretation These results demonstrate the value of epidemiological modeling and genome surveillance to assess mitigation strategies. At the same time, an active search for cryptic transmission TRANS clusters is crucial to interrupt local transmission TRANS of SARS-CoV-2 in a region.

    SARS-CoV-2 infection MESHD, disease MESHD and transmission TRANS in domestic cats

    Authors: Natasha N Gaudreault; Jessie D Trujillo; Mariano Carossino; David A Meekins; Igor Morozov; Daniel W Madden; Sabarish V Indran; Dashzeveg Bold; Velmurugan Balaraman; Taeyong Kwon; Bianca Libanori Artiaga; Konner Cool; Adolfo Garcia-Sastre; Wenjun Ma; William C Wilson; Jamie Henningson; Udeni BR Balasuriya; Juergen A Richt

    doi:10.1101/2020.08.04.235002 Date: 2020-08-04 Source: bioRxiv

    Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) is the cause of Coronavirus Disease MESHD 2019 (COVID-19) and responsible for the current pandemic. Recent SARS-CoV-2 susceptibility and transmission TRANS studies in cats show that the virus can replicate in these companion animals and transmit to other cats. Here, we present an in-depth study of SARS-CoV-2 infection MESHD, associated disease MESHD and transmission TRANS dynamics in domestic cats. Six 4- to 5-month-old cats were challenged with SARS-CoV-2 via intranasal and oral routes simultaneously. One day post challenge (DPC), two sentinel contact cats were co-mingled with the principal infected animals. Animals were monitored for clinical signs, clinicopathological abnormalities and viral shedding throughout the 21 DPC observation period. Postmortem examinations were performed at 4, 7 and 21 DPC to investigate disease progression MESHD. Viral RNA was not detected in blood SERO but transiently in nasal, oropharyngeal and rectal swabs and bronchoalveolar lavage fluid as well as various tissues. Tracheobronchoadenitis of submucosal glands with the presence of viral RNA and antigen was observed in airways of the infected cats on 4 and 7 DPC. Serology showed that both, principal and sentinel cats, developed SARS-CoV-2-specific and neutralizing antibodies to SARS-CoV-2 SERO detectable at 7 DPC or 10 DPC, respectively. All animals were clinically asymptomatic TRANS during the course of the study and capable of transmitting SARS-CoV-2 to sentinels within 2 days of comingling. The results of this study are critical for our understanding of the clinical course of SARS-CoV-2 in a naturally susceptible host species, and for risk assessment of the maintenance of SARS-CoV-2 in felines and transmission TRANS to other animals and humans.

    Containing the Spread of Infectious Disease MESHD on College Campuses

    Authors: Mirai Shah; Gabrielle Ferra; Susan Fitzgerald; Paul Barreira; Pardis Sabeti; Andres Colubri

    doi:10.1101/2020.07.31.20166348 Date: 2020-08-04 Source: medRxiv

    College campuses in the United States are highly vulnerable to infectious diseases MESHD outbreaks, and there is a mounting need to develop strategies that best mitigate their size and duration, particularly as colleges consider reopening their campuses in the midst of the COVID-19 pandemic. Towards addressing this need, we applied a stochastic transmission TRANS model to quantify the impact of university-level responses to past outbreaks on their campuses and used it to determine which control interventions are most effective. The model aims to simultaneously overcome three crucial issues: stochastic variation in small populations, missing or unobserved case data, and changes in disease MESHD transmission TRANS rates post-intervention. We tested the model and assessed various interventions using data from the 2014 and 2016 mumps MESHD outbreaks at Ohio State University and Harvard University, respectively. Our results suggest that universities should design more aggressive diagnostic procedures and stricter isolation policies to decrease infectious disease MESHD incidence on campus. Our model can be applied to data from other outbreaks in college campuses and similar small-population settings.

    A multi-centre prospective study of COVID-19 transmission TRANS following outpatient Gastrointestinal Endoscopy in the United Kingdom

    Authors: Bu'Hussain Hayee; - The SCOTS project group; James E East; Colin R Rees; Ian Penman

    doi:10.1101/2020.08.02.20166736 Date: 2020-08-04 Source: medRxiv

    Message The COVID-19 pandemic has severely curtailed the practice of endoscopy (as an exemplar for outpatient diagnostic procedures) worldwide. Restart and recovery processes will be influenced by the need to protect patients and staff from disease MESHD transmission TRANS, but data on the risk of COVID-19 transmission TRANS after endoscopy are sparse. This is of particular importance in later pandemic phases when the risk of harm from delayed or missed significant diagnoses is likely to far outweigh the risk of infection TRANS risk of infection TRANS infection MESHD. The British Society of Gastroenterology (BSG) guidance for restarting endoscopy included stratification of diagnostic procedures according to aerosol generation or assessment of infectious risk as well as pragmatic guidance on the use of personal protective equipment (PPE). We sought to document the risk of COVID-19 transmission TRANS after endoscopy in this 'COVID-minimised' environment. Prospective data were collected from 18 UK centres for n=6208 procedures, with follow-up telephone assessment of patients at 7 and 14 days. No cases of COVID-19 were documented by any centre after endoscopy in either patients or staff, with 3/2611 (0.11%) asymptomatic TRANS patients testing positive for SARS-CoV-2 on nasopharyngeal swab testing pre-endoscopy. While these data cannot determine the relative contribution of each component of a COVID-minimised pathway, they provide clear support for such an approach, are reassuring and should aid planning for outpatient diagnostics in the COVID-19 recovery phase.

    Fitting models to the COVID-19 outbreak and estimating R

    Authors: Matt J Keeling; Louise Dyson; Glen Guyver-Fletcher; Alex Holmes; Malcolm G Semple; - ISARIC4C Investigators; Michael J Tildesley; Edward M Hill

    doi:10.1101/2020.08.04.20163782 Date: 2020-08-04 Source: medRxiv

    The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease MESHD. Fitting mathematical models of infectious disease MESHD transmission TRANS to the available epidemiological data provides a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the basic reproductive ratio, $R$, has taken on special significance in terms of the general understanding of whether the epidemic is under control ($R<1$). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease MESHD outbreaks. Here, we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing SERO. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the timecourse of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.

    Extended lifetime of respiratory droplets in a turbulent vapour puff and its implications on airborne disease MESHD transmission TRANS

    Authors: Kai Leong Chong; Chong Shen Ng; Naoki Hori; Rui Yang; Roberto Verzicco; Detlef Lohse

    id:2008.01841v1 Date: 2020-08-04 Source: arXiv

    To mitigate the COVID-19 pandemic, it is key to slow down the spreading of the life-threatening coronavirus (SARS-CoV-2). This spreading mainly occurs through virus-laden droplets expelled at speaking, coughing MESHD coughing HP, sneezing MESHD sneezing HP, or even breathing. To reduce infections MESHD through such respiratory droplets, authorities all over the world have introduced the so-called "2-meter distance rule" or "6-foot rule". However, there is increasing empirical evidence, e.g. through the analysis of super-spreading events, that airborne transmission TRANS of the coronavirus over much larger distances plays a major role with tremendous implications for the risk assessment of coronavirus transmission TRANS. Here we employ direct numerical simulations of a typical respiratory aerosol in a turbulent jet of the respiratory event within a Lagrangian-Eulerian approach with 5000 droplets, coupled to the ambient velocity, temperature, and humidity fields to allow for exchange of mass and heat and to realistically account for the droplet evaporation under different ambient conditions. We found that for an ambient relative humidity RH of 50% the lifetime of the smallest droplets of our study with initial diameter of 10 um gets extended by a factor of more than 30 as compared to what is suggested by the classical picture of Wells, due to collective effects during droplet evaporation and the role of the respiratory humidity, while the larger droplets basically behave ballistically. With increasing ambient RH the extension of the lifetimes of the small droplets further increases and goes up to 150 times for 90% RH, implying more than two meters advection range of the respiratory droplets within one second. Smaller droplets live even longer and travel TRANS further. Our results may explain why COVID-19 superspreading events can occur for large ambient RH such as in cooled-down meat-processing plants or in pubs with poor ventilation.

    Epidemiological characteristics of SARS-COV-2 in Myanmar

    Authors: Aung Min Thway; Htun Tayza; Tun Tun Win; Ye Minn Tun; Moe Myint Aung; Yan Naung Win; Kyaw M Tun

    doi:10.1101/2020.08.02.20166504 Date: 2020-08-04 Source: medRxiv

    Coronavirus disease MESHD (COVID-19) is an infectious disease MESHD caused by a newly discovered severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2). In Myanmar, first COVID-19 reported cases were identified on 23rd March 2020. There were 336 reported confirmed cases TRANS, 261 recovered and 6 deaths MESHD through 13th July 2020. The study was a retrospective case series and all COVID-19 confirmed cases TRANS from 23rd March to 13th July 2020 were included. The data series of COVID-19 cases were extracted from the daily official reports of the Ministry of Health and Sports (MOHS), Myanmar and Centers for Disease MESHD Control and Prevention (CDC), Myanmar. Among 336 confirmed cases TRANS, there were 169 cases with reported transmission TRANS events. The median serial interval TRANS was 4 days (IQR 3, 2-5) with the range of 0 - 26 days. The mean of the reproduction number TRANS was 1.44 with (95% CI = 1.30-1.60) by exponential growth method and 1.32 with (95% CI = 0.98-1.73) confident interval by maximum likelihood method. This study outlined the epidemiological characteristics and epidemic parameters of COVID-19 in Myanmar. The estimation parameters in this study can be comparable with other studies and variability of these parameters can be considered when implementing disease MESHD control strategy in Myanmar.

    SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic

    Authors: Najia K Ghanchi; Kiran I Masood; Asghar Nasir; Waqasuddin Khan; Syed H Abidi; Saba Shahid; Syed F Mahmood; Akbar R Kanji; Safina A Razzak; Zeeshan Ansar; Nazneen Islam; Mohammad B Dharejo; Zahra Hasan; Rumina Hasan

    doi:10.1101/2020.08.04.234153 Date: 2020-08-04 Source: bioRxiv

    ObjectivesPakistan has a high infectious disease MESHD burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country. MethodsWe performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May. ResultsStrains from travelers clustered with those from China, Saudi Arabia, India, USA and Australia. Five of eight SARS-CoV-2 strains were GH clade with Spike glycoprotein D614G, Ns3 gene Q57H, and RNA dependent RNA polymerase (RdRp) P4715L mutations. Two were S (ORF8 L84S and N S202N) and three were L clade and one was an I clade strain. One GH and one L strain each displayed Orf1ab L3606F indicating further evolutionary transitions. ConclusionsThis data reveals SARS-CoV-2 strains of L, G, S and I have been circulating in Pakistan from March, at the start of the pandemic. It indicates viral diversity regarding infection MESHD in this populous region. Continuing molecular genomic surveillance of SARS-CoV-2 in the context of disease MESHD severity will be important to understand virus transmission TRANS patterns and host related determinants of COVID-19 in Pakistan.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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