Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (82)

Fever (62)

Cough (60)

Falls (26)

Respiratory distress (18)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 1173
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    Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

    Authors: Gregory Queromes; Gregory Destras; Antonin Bal; Hadrien Regue; Gwendolyne Burfin; Solenne Brun; Remi Fanget; Florence Morfin; Martine Valette; Bruno Lina; Emilie Frobert; Laurence Josset

    doi:10.1101/2020.08.07.241653 Date: 2020-08-10 Source: bioRxiv

    Through routine genomic surveillance of the novel SARS-CoV-2 virus (n=229 whole genome sequences), 2 different frameshifting deletions were newly detected in the open reading frame (ORF) 6, starting at the same position (27267). While the 26-nucleotide deletion variant was only found in one sample in March 2020, the 34-nucleotide deletion variant was found within a single geriatric hospital unit in 5/9 patients sequenced and one health care worker with samples collected between April 2nd and 9th, 2020. Both the presence of the 34-nucleotide deletion variant limited to this unit and the clustering of the corresponding whole genome sequences by phylogeny analysis strongly suggested a nosocomial transmission TRANS between patients. Interestingly, prolonged viral excretion of the 34-nucleotide deletion variant was identified in a stool sample 14 days after initial diagnosis for one patient. Clinical data revealed no significant difference in disease MESHD severity between patients harboring the wild-type or the 34-nucleotide deletion variants. The in vitro infection MESHD of the two deletion variants on primate endothelial kidney cells (BGM) and human lung adenocarcinoma MESHD lung adenocarcinoma HP cells (Calu-3) yielded comparable replication kinetics with the wild-type strain. Furthermore, high viral loads were found in vivo regardless of the presence or absence of the ORF6 deletion. Our study highlights the transmission TRANS and replication capacity of two newly described deletion variants in the same ORF6 region.

    How Efficient is Contact Tracing TRANS in Mitigating the Spread of Covid-19? A Mathematical Modeling Approach

    Authors: T. A. Biala; Y. O. Afolabi; A. Q. M. Khaliq

    id:2008.03859v1 Date: 2020-08-10 Source: arXiv

    Contact Tracing TRANS (CT) is one of the measures taken by government and health officials to mitigate the spread of the novel coronavirus. In this paper, we investigate its efficacy by developing a compartmental model for assessing its impact on mitigating the spread of the virus. We describe the impact on the reproduction number TRANS $\mathcal{R}_c$ of Covid-19. In particular, we discuss the importance and relevance of parameters of the model such as the number of reported cases, effectiveness of tracking and monitoring policy, and the transmission TRANS rates to contact tracing TRANS. We describe the terms ``perfect tracking'', ``perfect monitoring'' and ``perfect reporting'' to indicate that traced contacts TRANS will be tracked while incubating, tracked contacts are efficiently monitored so that they do not cause secondary infections MESHD, and all infected persons are reported, respectively. We consider three special scenarios: (1) perfect monitoring and perfect tracking of contacts of a reported case, (2) perfect reporting of cases and perfect monitoring of tracked reported cases and (3) perfect reporting and perfect tracking of contacts of reported cases. Furthermore, we gave a lower bound on the proportion of contacts to be traced TRANS to ensure that the effective reproduction, $\mathcal{R}_c$, is below one and describe $\mathcal{R}_c$ in terms of observable quantities such as the proportion of reported and traced TRANS cases. Model simulations using the Covid-19 data obtained from John Hopkins University for some selected states in the US suggest that even late intervention of CT may reasonably reduce the transmission TRANS of Covid-19 and reduce peak hospitalizations and deaths MESHD. In particular, our findings suggest that effective monitoring policy of tracked cases and tracking of traced contacts TRANS while incubating are more crucial than tracing TRANS more contacts.

    Prediction of Covid-19 Infections MESHD Through December 2020 for 10 US States Using a Two Parameter Transmission TRANS Model Incorporating Outdoor Temperature and School Re-Opening Effects

    Authors: Ty A Newell

    doi:10.1101/2020.08.06.20169896 Date: 2020-08-07 Source: medRxiv

    Covid-19 infection MESHD case predictions (total cases) are made for August through December 2020 for 10 US States (NY, WA, GA, IL, MN, FL, OH, MI, CA, and NC). A two-parameter model based on social distance index (SDI) and disease MESHD transmission TRANS efficiency (G) parameters is used to characterize SARS-CoV-2 disease MESHD disease spread TRANS spread. Current lack of coherent and coordinated US policy causes the US to follow a linear infection MESHD growth path with a limit cycle behavior that modulates the US between accelerating and decaying infection MESHD growth on either side of a linear growth path boundary. Four prediction cases are presented: 1) No school re-openings; fall HP season temperature effect 2) No school re-openings; no fall HP season temperature effect 3) School re-openings; fall HP season temperature effect 4) School re-openings; no fall HP season temperature effect Fall HP outdoor temperatures, in contrast to the 1918 pandemic, are predicted to be beneficial for dampening SARS-CoV-2 transmission TRANS in States as they pass through swing season temperature range of 70F to 50F. Physical re-opening of schools in September are predicted to accelerate infections MESHD. States with low current infectious case numbers (eg, NY) are predicted to be minimally impacted while States with high current infectious case numbers (eg, CA and FL) will be significantly impacted by school re-openings. Updated infection MESHD predictions will be posted monthly (Sept, Oct, Nov, Dec) with adjustments based on actual trends in SDI and G. Assessments related to outdoor temperature impact, school re-openings, and other public gathering re-openings will be discussed in updated reports.

    The effect of school closures and reopening strategies on COVID-19 infection MESHD dynamics in the San Francisco Bay Area: a cross-sectional survey and modeling analysis

    Authors: Jennifer R Head; Kristin Andrejko; Qu Cheng; Philip A Collender; Sophie Phillips; Anna Boser; Alexandra K Heaney; Christopher M Hoover; Sean L Wu; Graham R Northrup; Karen Click; Robert Harrison; Joseph A Lewnard; Justin V Remais

    doi:10.1101/2020.08.06.20169797 Date: 2020-08-07 Source: medRxiv

    Background Large-scale school closures have been implemented worldwide to curb the spread of COVID-19. However, the impact of school closures and re-opening on epidemic dynamics remains unclear. Methods We simulated COVID-19 transmission TRANS dynamics using an individual-based stochastic model, incorporating social- contact data TRANS of school- aged TRANS children TRANS during shelter-in-place orders derived from Bay Area (California) household surveys. We simulated transmission TRANS under observed conditions and counterfactual intervention scenarios between March 17-June 1, and evaluated various fall HP 2020 K-12 reopening strategies. Findings Between March 17-June 1, assuming children TRANS <10 were half as susceptible to infection MESHD as older children TRANS and adults TRANS, we estimated school closures averted a similar number of infections MESHD (13,842 cases; 95% CI: 6,290, 23,040) as workplace closures (15,813; 95% CI: 9,963, 22,617) and social distancing measures (7,030; 95% CI: 3,118, 11,676). School closure effects were driven by high school and middle school closures. Under assumptions of moderate community transmission TRANS, we estimate that fall HP 2020 school reopenings will increase symptomatic illness among high school teachers (an additional 40.7% expected to experience symptomatic infection MESHD, 95% CI: 1.9, 61.1), middle school teachers (37.2%, 95% CI: 4.6, 58.1), and elementary school teachers (4.1%, 95% CI: -1.7, 12.0). Results are highly dependent on uncertain parameters, notably the relative susceptibility and infectiousness of children TRANS, and extent of community transmission TRANS amid re-opening. The school-based interventions needed to reduce the risk to fewer than an additional 1% of teachers infected varies by grade level. A hybrid-learning approach with halved class sizes of 10 students may be needed in high schools, while maintaining small cohorts of 20 students may be needed for elementary schools. Interpretation Multiple in-school intervention strategies and community transmission TRANS reductions, beyond the extent achieved to date, will be necessary to avoid undue excess risk associated with school reopening. Policymakers must urgently enact policies that curb community transmission TRANS and implement within-school control measures to simultaneously address the tandem health crises posed by COVID-19 and adverse child TRANS health and development consequences of long-term school closures.

    Wrong person, place and time: viral load and contact network structure predict SARS-CoV-2 transmission TRANS and super-spreading events

    Authors: Ashish Goyal; Daniel B Reeves; E. Fabian Cardozo-Ojeda; Joshua T Schiffer; Bryan T. Mayer

    doi:10.1101/2020.08.07.20169920 Date: 2020-08-07 Source: medRxiv

    SARS-CoV-2 is difficult to contain because most transmissions TRANS occur during the pre-symptomatic phase of infection MESHD. Moreover, in contrast to influenza, while most SARS-CoV-2 infected people do not transmit the virus to anybody, a small percentage secondarily infect large numbers of people. We designed mathematical models of SARS-CoV-2 and influenza which link observed viral shedding patterns with key epidemiologic features of each virus, including distributions of the number of secondary cases TRANS attributed to each infected person (individual R0 TRANS) and the duration between symptom onset TRANS in the transmitter and secondarily infected person ( serial interval TRANS). We identify that people with SARS-CoV-2 or influenza infections MESHD are usually contagious for fewer than two days congruent with peak viral load several days after infection MESHD, and that transmission TRANS is unlikely below a certain viral load. SARS-CoV-2 super-spreader events with over 10 secondary infections MESHD occur when an infected person is briefly shedding at a very high viral load and has a high concurrent number of exposed contacts. The higher predisposition of SARS-CoV-2 towards super-spreading events is not due to its 1-2 additional weeks of viral shedding relative to influenza. Rather, a person infected with SARS-CoV-2 exposes more people within equivalent physical contact networks than a person infected with influenza, likely due to aerosolization of virus. Our results support policies that limit crowd size in indoor spaces and provide viral load benchmarks for infection MESHD control and therapeutic interventions intended to prevent secondary transmission TRANS.

    SARS-CoV-2 infection MESHD, neuropathogenesis and transmission TRANS among deer mice: Implications for reverse zoonosis MESHD to New World rodents

    Authors: Anna Fagre; Juliette Lewis; Miles Eckley; Shijun Zhan; Savannah M Rocha; Nicole R Sexton; Bradly Burke; Brian J Geiss; Olve Peersen; Rebekah Kading; Joel Rovnak; Gregory D Ebel; Ronald B Tjalkens; Tawfik Aboellail; Tony Schountz

    doi:10.1101/2020.08.07.241810 Date: 2020-08-07 Source: bioRxiv

    Coronavirus disease MESHD-19 (COVID-19) emerged in November, 2019 in China and rapidly became pandemic. As with other coronaviruses, a preponderance of evidence suggests the virus originated in horseshoe bats (Rhinolophus spp.) and likely underwent a recombination event in an intermediate host prior to entry into human populations. A significant concern is that SARS-CoV-2 could become established in secondary reservoir hosts outside of Asia. To assess this potential, we challenged deer mice (Peromyscus maniculatus) with SARS-CoV-2 and found robust virus replication in the upper respiratory tract, lungs and intestines, with detectable viral RNA for up to 21 days in oral swabs and 14 days in lungs. Virus entry into the brain also occurred, likely via gustatory-olfactory-trigeminal pathway with eventual compromise to the blood SERO brain barrier. Despite this, no conspicuous signs of disease MESHD were observed and no deer mice succumbed to infection MESHD. Expression of several innate immune response genes were elevated in the lungs, notably IFN, Cxcl10, Oas2, Tbk1 and Pycard. Elevated CD4 and CD8{beta} expression in the lungs was concomitant with Tbx21, IFN{gamma} and IL-21 expression, suggesting a type I inflammatory immune response. Contact transmission TRANS occurred from infected to naive deer mice through two passages, showing sustained natural transmission TRANS. In the second deer mouse passage, an insertion of 4 amino acids occurred to fixation in the N-terminal domain of the spike protein that is predicted to form a solvent-accessible loop. Subsequent examination of the source virus from BEI Resources indicated the mutation was present at very low levels, demonstrating potent purifying selection for the insert during in vivo passage. Collectively, this work has determined that deer mice are a suitable animal model for the study of SARS-CoV-2 pathogenesis, and that they have the potential to serve as secondary reservoir hosts that could lead to periodic outbreaks of COVID-19 in North America.

    On the Interplay of Regional Mobility, Social Connectedness, and the Spread of COVID-19 in Germany

    Authors: Cornelius Fritz; Göran Kauermann

    id:2008.03013v1 Date: 2020-08-07 Source: arXiv

    Since the primary mode of respiratory virus transmission TRANS is person-to-person interaction, we are required to reconsider physical interaction patterns to mitigate the number of people infected with COVID-19. While non-pharmaceutical interventions (NPI) had an evident impact on national mobility patterns, only the relative regional mobility behaviour enables an unbiased perspective on the effect of human movement on the spread of COVID-19. In this paper we therefore investigate the impact of human mobility and social connectivity derived from Facebook activities on the weekly rate of new infections MESHD in Germany between March 3rd and June 22nd, 2020. Our results confirm that reduced social activity lowers the infection MESHD rate, accounting for regional and temporal patterns. The extent of social distancing, quantified by the percentage of people staying put within a federal administrative district, has an overall negative effect on the incidence of infections MESHD. Additionally, our results show spatial infection MESHD patterns based on geographic as well as social distances.

    CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic TRANS individuals uncovers a shift in viral prevalence SERO among a university population

    Authors: Jennifer N Rauch; Eric Valois; Jose Carlos Ponce-Rojas; Zach Aralis; Ryan L Lach; Francesca Zappa; Morgane Audouard; Sabrina C Solley; Chinmay Vaidya; Michael Costello; Holly Smith; Ali Javanbakht; Betsy Malear; Laura Polito; Stewart Comer; Katherine Arn; Kenneth S Kosik; Diego Acosta-Alvear; Maxwell Z Wilson; Lynn Fitzgibbons; Carolina Arias

    doi:10.1101/2020.08.06.20169771 Date: 2020-08-07 Source: medRxiv

    Background: The progress of the COVID-19 pandemic profoundly impacts the health of communities around the world, with unique impacts on colleges and universities. Transmission TRANS of SARS-CoV-2 by asymptomatic TRANS people is thought to be the underlying cause of a large proportion of new infections MESHD. However, the local prevalence SERO of asymptomatic TRANS and pre-symptomatic carriers TRANS of SARS-CoV-2 is influenced by local public health restrictions and the community setting. Objectives: This study has three main objectives. First, we looked to establish the prevalence SERO of asymptomatic TRANS SARS-CoV-2 infection MESHD on a university campus in California. Second, we sought to assess the changes in viral prevalence SERO associated with the shifting community conditions related to non-pharmaceutical interventions (NPIs). Third, we aimed to compare the performance SERO of CRISPR- and PCR-based assays for large-scale virus surveillance sampling in COVID-19 asymptomatic TRANS persons. Methods: We enrolled 1,808 asymptomatic TRANS persons for self-collection of oropharyngeal (OP) samples to undergo SARS-CoV-2 testing. We compared viral prevalence SERO in samples obtained in two time periods: May 28th-June 11th; June 23rd-July 2nd. We detected viral genomes in these samples using two assays: CREST, a CRISPR-based method recently developed at UCSB, and the RT-qPCR test recommended by US Centers for Disease MESHD Control and Prevention (CDC). Results: Of the 1,808 participants, 1,805 were affiliates of the University of California, Santa Barbara, and 1,306 were students. None of the tests performed on the 732 samples collected between late May to early June were positive. In contrast, tests performed on the 1076 samples collected between late June to early July, revealed nine positive cases. This change in prevalence SERO met statistical significance, p = 0.013. One sample was positive by RT-qPCR at the threshold of detection, but negative by both CREST and CLIA-confirmation testing. With this single exception, there was perfect concordance in both positive and negative results obtained by RT-qPCR and CREST. The estimated prevalence SERO of the virus, calculated using the confirmed cases TRANS, was 0.74%. The average age TRANS of our sample population was 28.33 (18-75) years, and the average age TRANS of the positive cases was 21.7 years (19-30). Conclusions: Our study revealed that there were no COVID-19 cases in our study population in May/June. Using the same methods, we demonstrated a substantial shift in prevalence SERO approximately one month later, which coincided with changes in community restrictions and public interactions. This increase in prevalence SERO, in a young and asymptomatic TRANS population which would not have otherwise accessed COVID-19 testing, indicated the leading wave of a local outbreak, and coincided with rising case counts in the surrounding county and the state of California. Our results substantiate that large, population-level asymptomatic TRANS screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPR- and PCR-based assays indicate expanded options for surveillance testing

    Transient dynamics of SARS-CoV-2 as England exited national lockdown

    Authors: Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott

    doi:10.1101/2020.08.05.20169078 Date: 2020-08-06 Source: medRxiv

    Control of the COVID-19 pandemic requires a detailed understanding of prevalence SERO of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission TRANS antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence SERO data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic TRANS individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence SERO from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic TRANS at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age TRANS patterns of infection MESHD changed between rounds, with a reduction by a factor of five in prevalence SERO in 18 to 24 year olds. Our data were suggestive of increased risk of infection TRANS risk of infection TRANS infection MESHD in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection MESHD intensity in and near London. Under multiple sensitivity SERO analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence SERO and a shift in the pattern of infection MESHD by age TRANS and occupation. Community-based sampling, including asymptomatic TRANS individuals, is necessary to fully understand the nature of ongoing transmission TRANS.

    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.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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