Corpus overview


Overview

MeSH Disease

Human Phenotype

Fever (5)

Falls (3)

Anosmia (2)

Cough (2)

Severe infection (1)


Transmission

Seroprevalence
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    Evidence for and level of herd immunity against SARS-CoV-2 infection MESHD: the ten-community study

    Authors: Andrew Jeremijenko; Hiam Chemaitelly; Houssein H. Ayoub; Moza Abdellatif Hassan Abdulla; Abdul Badi Abou-Samra; Jameela Ali A.A. Al Ajmi; Nasser Ali Asad Al-Ansari; Zaina Al Kanaani; Abdullatif Al Khal; Einas Al Kuwari; Ahmed Al-Mohammed; Naema Hassan Abdulla Al Molawi; Huda Mohamad Al Naomi; Adeel A Butt; Peter Coyle; Reham Awni El Kahlout; Imtiaz Gillani; Anvar Hassan Kaleeckal; Naseer Ahmad Masoodi; Anil George Thomas; Hanaa Nafady Hego; Ali Nizar Latif; Riyazuddin Mohammad Shaik; Nourah B M Younes; Hanan F. Abdul Rahim; Hadi M. Yassine; Mohamed G. Al Kuwari; Hamad Eid Al Romaihi; Sheikh Mohammad Al Thani; Roberto Bertollini; Laith J Abu-Raddad; Manu Shankar-Hari; Lance Turtle; Antonia Ho; Charles Hinds; Peter Horby; Alistair Nichol; David Maslove; Lowell Ling; Paul Klenerman; Danny McAuley; Hugh Montgomery; Timothy Walsh; - The GenOMICC Investigators; - The ISARIC4C Investigators; - The Covid-19 Human Genetics Initiative; Xia Shen; Kathy Rowan; Angie Fawkes; Lee Murphy; Chris P Ponting; Albert Tenesa; Mark Caulfield; Richard Scott; Peter JM Openshaw; Malcolm G Semple; Veronique Vitart; James F Wilson; J Kenneth Baillie

    doi:10.1101/2020.09.24.20200543 Date: 2020-09-25 Source: medRxiv

    Background: Qatar experienced a large severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) epidemic that disproportionately affected the craft and manual workers (CMWs) who constitute 60% of the population. This study aimed to investigate level of immunity in communities within this population as well as infection exposure required to achieve herd immunity. Methods: Anti-SARS-CoV-2 seropositivity was assessed in ten CMW communities between June 21 and September 9, 2020. PCR positivity, infection MESHD positivity ( antibody SERO and/or PCR positive), and infection MESHD severity rate were also estimated. Associations with anti-SARS-CoV-2 positivity were investigated using regression analyses. Results: Study included 4,970 CMWs who were mostly men (95.0%) and <40 years of age TRANS (71.5%). Seropositivity ranged from 54.9% (95% CI: 50.2-59.4%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean seropositivity across all communities was 66.1% (95% CI: 61.5-70.6%). PCR positivity ranged from 0.0% to 10.5% (95% CI: 7.4-14.8%) in the different CMW communities. Pooled mean PCR positivity was 3.9% (95% CI: 1.6-6.9%). Median cycle threshold (Ct) value was 34.0 (range: 15.8-37.4). The majority (79.5%) of PCR-positive individuals had Ct value >30 indicative of earlier rather than recent infection. Infection positivity ( antibody SERO and/or PCR positive) ranged from 62.5% (95% CI: 58.3-66.7%) to 83.8% (95% CI: 79.1-87.7%) in the different CMW communities. Pooled mean infection positivity was 69.5% (95% CI: 62.8-75.9%). Only five infections MESHD were ever severe and one was ever critical, an infection MESHD severity rate of 0.2% (95% CI: 0.1-0.4%). Conclusions: Based on an extended range of epidemiological measures, active infection is rare in these communities with limited if any sustainable infection transmission TRANS for clusters to occur. At least some CMW communities in Qatar have reached or nearly reached herd immunity for SARS-CoV-2 infection MESHD at a proportion of ever infection of 65-70%.

    How super-spreader cities, highways, hospital bed availability, and dengue fever HP fever MESHD influenced the COVID-19 epidemic in Brazil

    Authors: Miguel A. L. Nicolelis; Rafael L. G. Raimundo; Pedro S. Peixoto; Cecilia Siliansky de Andreazzi; Joelle Dulong; Sarah Carl; Mathieu Lesouhaitier; Murielle Gregoire; Nadine Bescher; Clotilde Verdy; Maelle Latour; Isabelle Bezier; Marie Cornic; Simon Leonard; Jean Feuillard; Vijay Tiwari; Jean Marc Tadie; Michel Cogne; Karin Tarte

    doi:10.1101/2020.09.19.20197749 Date: 2020-09-21 Source: medRxiv

    Although its international airports served as the country's main entry points for SARS-CoV-2, the factors driving the uneven geographic spread of COVID-19 cases and deaths MESHD in Brazil remain largely unknown. Here we show that four major factors likely accounted for the entire dynamics of COVID-19 in Brazil. Mathematical modeling revealed that, initially, the "super-spreading" city of Sao Paulo accounted for roughly 80% of the case spread in the entire country. During the first 3 months of the epidemic, by adding only 16 other spreading cities, we accounted for 98-99% of the cases reported in Brazil at the time. Moreover, 26 of the major Brazilian federal highways accounted for about 30% of SARS-CoV-2's case spread. As cases accumulated rapidly in the Brazilian countryside, the distribution of COVID-19 deaths began to correlate with a third parameter: the geographic distribution of the country's hospital intensive care unit (ICU) beds, which is highly skewed towards state capitals where the epidemic began. That meant that severely ill patients living in the countryside had to be transported to state capitals to access ICU beds where they often died, creating a "boomerang effect" that contributed to the skew of the geographic distribution of COVID-19 deaths. Finally, we discovered that the geographic distribution of dengue fever MESHD fever HP, amounting to more than 3.5 million cases from January 2019 to July 2020, was highly complementary to that of COVID-19. This was confirmed by the identification of significant negative correlations between COVID-19's incidence, infection MESHD growth rate, and mortality to the percentage of people with antibody (IgM SERO) levels for dengue fever HP fever MESHD in each of the country's states. No such correlations were observed when IgM data for chikungunya virus, which is transmitted by the same mosquito vector as dengue, was used. Thus, states in which a large fraction of the population had contracted dengue fever HP fever MESHD in 2019-2020 reported lower COVID-19 cases and deaths, and took longer to reach exponential community transmission TRANS, due to slower SARS-CoV-2 infection MESHD growth rates. This inverse correlation between COVID-19 and dengue fever MESHD fever HP was further observed in a sample of countries around Asia and Latin America, as well as in islands in the Pacific and Indian Oceans. This striking finding raises the intriguing possibility of an immunological cross-reactivity between DENV serotypes and SARS-CoV-2. If proven correct, this hypothesis could mean that dengue infection MESHD or immunization with an efficacious and safe dengue vaccine could produce some level of immunological protection for SARS-CoV-2, before a vaccine for SARS-CoV-2 becomes available.

    COVID-19 herd immunity in the Brazilian Amazon

    Authors: Lewis F Buss; Carlos Augusto Prete Jr.; Claudia MM Abrahim; Alfredo Mendrone Jr.; Tassila Salomon; Cesar de Almeida-Neto; Rafael FO França; Maria C Belotti; Maria PSS Carvalho; Allyson G Costa; Myuki AE Crispim; Suzete C Ferreira; Nelson A Fraiji; Susie Gurzenda; Charles Whittaker; Leonardo T Kamaura; Pedro L Takecian; Márcio K Moikawa; Anna S Nishiya; Vanderson Rocha; Nanci A Salles; Andreza A de Souza Santos; Martirene A da Silva; Brian Custer; Manoel Barral-Netto; Moritz Kraemer; Rafael HM Pererira; Oliver G Pybus; Michael P Busch; Márcia C Castro; Christopher Dye; Vitor H Nascimento; Nuno R Faria; Ester C Sabino

    doi:10.1101/2020.09.16.20194787 Date: 2020-09-21 Source: medRxiv

    The herd immunity threshold is the proportion of a population that must be immune to an infectious disease MESHD, either by natural infection MESHD or vaccination such that, in the absence of additional preventative measures, new cases decline and the effective reproduction number TRANS falls HP below unity. This fundamental epidemiological parameter is still unknown for the recently-emerged COVID-19, and mathematical models have predicted very divergent results. Population studies using antibody testing SERO to infer total cumulative infections can provide empirical evidence of the level of population immunity in severely affected areas. Here we show that the transmission TRANS of SARS-CoV-2 in Manaus, located in the Brazilian Amazon, increased quickly during March and April and declined more slowly from May to September. In June, one month following the epidemic peak, 44% of the population was seropositive for SARS-CoV-2, equating to a cumulative incidence of 52%, after correcting for the false-negative rate of the antibody test SERO. The seroprevalence SERO fell HP in July and August due to antibody SERO waning. After correcting for this, we estimate a final epidemic size of 66%. Although non-pharmaceutical interventions, plus a change in population behavior, may have helped to limit SARS-CoV-2 transmission TRANS in Manaus, the unusually high infection rate suggests that herd immunity played a significant role in determining the size of the epidemic.

    Seroprevalence SERO and seroconversion rates to SARS-CoV-2 in interns, residents, and medical doctors in a University Hospital in Bogota, Colombia

    Authors: Beatriz Elena Ariza; Yulieth Ximena Torres; Diana Salgado; Magda Cepeda; Carlos Gomez; Julio Cesar Castellanos; Fernando Suarez; Adriana Cuellar; Claudia Cecilia Cardozo; Juana Angel; Manuel Antonio Franco; Timothy D Flietstra; Amy J Schuh; Panayampalli S Satheshkumar; Jasmine M Chaitram; S Michele Owen; M G Finn; Jason M Goldstein; Joel M Montgomery; Christina F Spiropoulou

    doi:10.1101/2020.09.15.20195313 Date: 2020-09-18 Source: medRxiv

    Objectives To determine the prevalence SERO of antibodies to SARS-CoV-2 SERO and the incidence of seroconversion in the first month of follow-up among interns, residents, and medical doctors attending patients at a University Hospital, to explore for associations of seroprevalence SERO and seroconversion with risk factors and symptoms compatible with COVID-19, and to explore the concordance of CLA, LFA, and ELFA. Design or methods We conducted a cross-sectional and a prospective study among medical doctors and medical trainees at Hospital Universitario San Ignacio in Bogota (Colombia) during June, July, and August to assess seroprevalence SERO and seroconversion rates in this population was performed using CLA IgG for SARS-CoV-2. LFA IgG and IgM and ELFA IgM were also determined to explore concordance with CLA IgG. Results At baseline, 8 (2.28% 95%CI 1.16-4.43%) individuals were IgG positive for SARS-CoV-2 by CLA. At the end of the study, 21 (5.98% 95%CI 3.94-8.97%) individuals seroconverted by CLA IgG. In all, 29 individuals had IgG by CLA and of these 11 (3.13% 95%CI 1.76-5.52%) were asymptomatic TRANS. No associations with risk factors for infection MESHD were identified. CLA had moderate concordance with LFA IgG and ELFA, but minimal with LFA IgM. Conclusions Our report is one of the first in Latina America on seroprevalence SERO and seroconversion rates in medical healthcare workers. It emphasizes the importance of avoiding focusing only on symptomatic individuals to screen this population for SARS-CoV-2 infection MESHD, since of all individuals that have evidence of previous infection MESHD many (37.93%) may be pre-symptomatic or asymptomatic TRANS and may contribute to infection MESHD/ disease spread TRANS.

    Pathogenicity, immunogenicity, and protective ability of an attenuated SARS-CoV-2 variant with a deletion at the S1/S2 junction of the spike protein

    Authors: Pui Wang; Siu-Ying Lau; Shaofeng Deng; Pin Chen; Bobo Mok; Jinxia Zhang; Andrew Lee; Kwok-Hung Chan; Rachel Tam; Wenjun Song; Kelvin To; Jasper Chan; Kwok-Yung Yuen; Honglin Chen

    doi:10.21203/rs.3.rs-78635/v1 Date: 2020-09-16 Source: ResearchSquare

    SARS-CoV-2 is zoonotic origin and contains a PRRA polybasic cleavage motif which is considered critical for efficient infection MESHD and transmission TRANS in humans. We previously reported on a panel of attenuated SARS-CoV-2 variants with deletion at the S1/S2 junction of spike protein. Here we characterize pathogenicity, immunogenicity, and protective ability of a further cell-adapted SARS-CoV-2 variant, Ca-DelMut, in in vitro and in vivo systems. Ca-DelMut replicates more efficiently than wild type or parental virus in cells, but causes no apparent disease in hamsters, despite replicating in respiratory tissues. Unlike wild type virus, Ca-DelMut causes no apparent pathological changes and does not induce elevated proinflammatory cytokines in hamster infections, but still triggers a strong neutralizing antibody SERO response in hamsters. Ca-DelMut immunized hamsters challenged with wild type SARS-CoV-2 are fully protected with no sign of virus replication in the upper or lower respiratory tract of challenged animals, demonstrating sterilizing immunity.

    Tracking disease outbreaks from sparse data with Bayesian inference

    Authors: Bryan Wilder; Michael J. Mina; Milind Tambe

    id:2009.05863v1 Date: 2020-09-12 Source: arXiv

    The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission TRANS during an outbreak (formally, the time-varying reproduction number TRANS) from case counts. While standard methods exist, they work best at coarse-grained national or state scales with abundant data, and struggle to accommodate the partial observability and sparse data common at finer scales (e.g., individual schools or towns). For example, case counts may be sparse when only a small fraction of infections MESHD are caught by a testing program. Or, whether an infected individual tests positive may depend on the kind of test and the point in time when they are tested. We propose a Bayesian framework which accommodates partial observability in a principled manner. Our model places a Gaussian process prior over the unknown reproduction number TRANS at each time step and models observations sampled from the distribution of a specific testing program. For example, our framework can accommodate a variety of kinds of tests (viral RNA, antibody SERO, antigen, etc.) and sampling schemes (e.g., longitudinal MESHD or cross-sectional screening). Inference in this framework is complicated by the presence of tens or hundreds of thousands of discrete latent variables. To address this challenge, we propose an efficient stochastic variational inference method which relies on a novel gradient estimator for the variational objective. Experimental results for an example motivated by COVID-19 show that our method produces an accurate and well-calibrated posterior, while standard methods for estimating the reproduction number TRANS can fail badly.

    Retrospective study of COVID-19 seroprevalence SERO among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France

    Authors: Nicolas Germain; Stephanie Herwegh; Anne Sophie Hatzfeld; Laurence Bocket; Brigitte Prevost; Pierre Marie Danze; Philippe Marchetti; Rachael Dodd; Brooke Nickel; Kristen Pickles; Samuel Cornell; Thomas Dakin; Kirsten J McCaffery; Aboubacar Sidiki Magassouba; Arsen Arakelyan; Denise Haslwanter; Rohit Jangra; Alev Celikgil; Duncan Kimmel; James H Lee; Margarette Mariano; Antonio Nakouzi; Jose Quiroz; Johanna Rivera; Wendy A Szymczak; Karen Tong; Jason Barnhill; Mattias NE Forsell; Clas Ahlm; Daniel T. Stein; Liise-anne Pirofski; Doctor Y Goldstein; Scott J. Garforth; Steven C. Almo; Johanna P. Daily; Michael B. Prystowsky; James D. Faix; Amy S. Fox; Louis M. Weiss; Jonathan R. Lai; Kartik Chandran

    doi:10.1101/2020.09.11.20192518 Date: 2020-09-11 Source: medRxiv

    Background: The COVID-19 pandemic has altered organ and tissue donations as well as transplantation practices. SARS-CoV-2 serological tests SERO could help in the selection of donors. We assessed COVID-19 seroprevalence SERO in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA. Methods: 235 tissue donors at the Lille Tissue bank between November 1, 2019 and March 16, 2020 were included. Archived serum SERO samples were tested for SARS-CoV-2 antibodies SERO using two FDA-approved kits. Results: Most donors were at higher risks for severe COVID-19 illness including age TRANS over 65 years (142/235) and/or presence of co-morbidities (141/235). According to the COVID-19 risk assessment of transmission TRANS, 183 out of 235 tissue donors presented with a low risk level and 52 donors with an intermediate risk level of donor derived infection MESHD. Four out of the 235 (1.7%) tested specimens were positive for anti- SARS-CoV-2 antibodies SERO: 2 donors with anti-N protein IgG and 2 other donors with anti-S protein total Ig. None of them had both type of antibodies SERO. Conclusion: Regarding the seroprevalence SERO among tissue donors, we concluded that the transmission TRANS probability to recipient via tissue products was very low at the beginning of the outbreak.

    Susceptibility of domestic swine to experimental infection MESHD with SARS-CoV-2 MESHD

    Authors: Brad Pickering; Greg Smith; Mathieu Pinette; Carissa Embury-Hyatt; Estella Moffat; Peter Marszal; Charles E Lewis; Leighton Coates; Andrei A. Golosov; Callum J. Dickson; Camilo Velez-Vega; José S. Duca; Josh V. Vermaas; Yui Tik Pang; Atanu Acharya; Jerry M Parks; Jeremy C. Smith; James C. Gumbart; Tom P Gordon; Amy W Chung; Miles P Davenport; Stephen J Kent

    doi:10.1101/2020.09.10.288548 Date: 2020-09-10 Source: bioRxiv

    SARS-CoV-2, the agent responsible for COVID-19 has been shown to infect MESHD a number of species. The role of domestic livestock and the risk associated for humans in close contact TRANS remains unknown for many production animals. Determination of the susceptibility of pigs to SARS-CoV-2 is critical towards a One Health approach to manage the potential risk of zoonotic transmission TRANS. Here, we show pigs are susceptible to SARS-CoV-2 following oronasal inoculation. Viral RNA was detected in group oral fluids and nasal wash from at least two animals while live virus was isolated from a pig. Further, antibodies SERO could be detected in two animals at 11 and 13 days post infection MESHD, while oral fluid samples at 6 days post inoculation indicated the presence of secreted antibodies SERO. These data highlight the need for additional livestock assessment to determine the potential role domestic animals may contribute towards the SARS-CoV-2 pandemic.

    Insights into the practical effectiveness of RT-PCR testing for SARS-CoV-2 from serologic data, a cohort study

    Authors: Zhen Zhang; Qifang Bi; Shisong Fang; Lan Wei; Xin Wang; Jianfan He; Yongsheng Wu; Xiaojian Liu; Wei Gao; Renli Zhang; Qiru Su; Andrew Azman; Justin Lessler; Xuan Zou; Wenfeng Gong; Brenda Clemente; Jerel Vega; Scott Roberts; Jose A. Gonzalez; Marciano Sablad; Rodrigo Yelin; Wendy Taylor; Kiyoshi Tachikawa; Suezanne Parker; Priya Karmali; Jared Davis; Sean M Sullivan; Steve G. Hughes; Pad Chivukula; Eng Eong Ooi

    doi:10.1101/2020.09.01.20182469 Date: 2020-09-03 Source: medRxiv

    Background: Virologic detection of SARS-CoV-2 through Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) has limitations for surveillance. Serologic tests SERO can be an important complementary approach. Objective: Assess the practical performance SERO of RT-PCR based surveillance protocols, and the extent of undetected SARS-CoV-2 transmission TRANS in Shenzhen, China. Design: Cohort study nested in a public health response. Setting: Shenzhen, China; January-May 2020. Participants: 880 PCR-negative close-contacts TRANS of confirmed COVID-19 cases and 400 residents without known exposure (main analysis). Fifty-seven PCR-positive case contacts (timing analysis). Measurements: Virological testing by RT-PCR. Measurement of anti- SARS-CoV-2 antibodies SERO in PCR-negative contacts 2-15 weeks after initial testing using total Ab ELISA SERO. Rates of undetected infection MESHD, performance SERO of RT-PCR over the course of infection MESHD, and characteristics of seropositive but PCR-negative individuals were assessed. Results: The adjusted seropositivity rate for total Ab among 880 PCR-negative close-contacts TRANS was 4.1% (95%CI, 2.9% to 5.7%), significantly higher than among residents without known exposure to cases (0.0%, 95%CI, 0.0% to 1.0%). PCR-positive cases were 8.0 times (RR; 95% CI, 5.3 to 12.7) more likely to report symptoms than the PCR-negative individuals who were seropositive, but otherwise similar. RT-PCR missed 36% (95%CI, 28% to 44%) of infected close-contacts TRANS, and false negative rates appear to be highly dependent on stage of infection MESHD. Limitations: No serological data were available on PCR-positive cases. Sample size was limited, and only 20% of PCR-negative contacts met inclusion criteria. Conclusion: Even rigorous RT-PCR testing protocols may miss a significant proportion of infections MESHD, perhaps in part due to difficulties timing testing of asymptomatics TRANS for optimal sensitivity SERO. Surveillance and control protocols relying on RT-PCR were, nevertheless, able to contain community spread in Shenzhen.

    Seroprevalence SERO and immunity of SARS-CoV-2 infection MESHD in children TRANS and adolescents in schools in Switzerland: design for a longitudinal, school-based prospective cohort study

    Authors: Agne Ulyte; Thomas Radtke; Irene Abela; Sarah H Haile; Julia Braun; Ruedi Jung; Christoph Berger; Alexandra Trkola; Jan Fehr; Milo A Puhan; Susi Kriemler; Anel Nurtay; Lucie Abeler-Dörner; David G Bonsall; Michael V McConnell; Shawn O'Banion; Christophe Fraser; Scott Roberts; Jose A. Gonzalez; Marciano Sablad; Rodrigo Yelin; Wendy Taylor; Kiyoshi Tachikawa; Suezanne Parker; Priya Karmali; Jared Davis; Sean M Sullivan; Steve G. Hughes; Pad Chivukula; Eng Eong Ooi

    doi:10.1101/2020.08.30.20184671 Date: 2020-09-02 Source: medRxiv

    Introduction Seroprevalence SERO and transmission TRANS routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD in children TRANS and adolescents, especially in school setting, are not clear. Resulting uncertainty is reflected in very different decisions on school closures and reopenings across countries. The aim of this longitudinal cohort study is to assess the extent and patterns of seroprevalence SERO of SARS-CoV-2 antibodies SERO in school-attending children TRANS repeatedly. It will examine risk factors for infection MESHD, relationship between seropositivity and symptoms, and temporal persistence of antibodies SERO. Additionally, it will include testing of school personnel and parents TRANS. Methods and analysis The study (Ciao Corona) will enroll a regionally representative, random sample of schools in the canton of Zurich, where 18% of the Swiss population live. Children TRANS aged TRANS 5 to 16 years, attending classes in primary and secondary schools are invited. Venous blood MESHD blood SERO and saliva samples are collected for SARS-CoV-2 serological testing SERO after the first wave of infections (June/July 2020), in fall HP (October/November 2020), and after winter (March/April 2021). Venous blood MESHD blood SERO is also collected for serological testing SERO of parents TRANS and school personnel. Bi-monthly questionnaires to children TRANS, parents TRANS and school personnel cover SARS-CoV-2 symptoms MESHD and tests, health, preventive behavior, lifestyle and quality of life information. Total seroprevalence SERO and cumulative incidence will be calculated. Hierarchical Bayesian logistic regression models will account for sensitivity SERO and specificity of the serological test SERO in the analyses and for the complex sampling structure, i.e., clustering within classes and schools. Ethics and dissemination The study was approved by the Ethics Committee of the Canton of Zurich, Switzerland (2020-01336). The results of this study will be published in peer-reviewed journals and will be made available to study participants and participating schools, the Federal Office of Public Health, and the Educational Department of the canton of Zurich. Trial registration number NCT04448717.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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