Corpus overview


MeSH Disease

Human Phenotype

Fever (24)

Cough (21)

Pneumonia (18)

Fatigue (10)

Falls (6)


    displaying 1 - 10 records in total 177
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    Modelling optimal vaccination strategy for SARS-CoV-2.

    Authors: Sam Moore; Edward M Hill; Louise Dyson; Michael Tildesley; Matt J Keeling; Itse Yusuf Nyam; Bamidele Iwalokun; Chika Onwuamah; Mabel Uwandu; Babatunde Lawal Salako; Akinola Abayomi; Akin Osibogun; Abimbola Bowale; Bodunrin Osikomaiya; Babafemi Thomas; Bamidele Mutiu; Nkiruka Nnonyelum Odunukwe

    doi:10.1101/2020.09.22.20194183 Date: 2020-09-24 Source: medRxiv

    The COVID-19 outbreak has highlighted our vulnerability to novel infections. Faced with this threat and no effective treatment, most countries adopted some form of enforced social distancing (lockdown) to reduce transmission TRANS - in most cases successfully reducing the reproductive number,R TRANS, below one. However, given the large pool of susceptible individuals that remain, complete relaxation of controls is likely to generate a substantial second wave. Vaccination remains the only foreseeable means of both containing the infection MESHD and returning to normal interactions and behaviour. Here, we consider the optimal targeting of vaccination with the aim of minimising future deaths MESHD or quality adjusted life year (QALY) losses. We show that, for a range of assumptions on the action and efficacy of the vaccine, targeting older age groups TRANS first is optimal and can avoid a second wave if the vaccine prevents transmission TRANS as well as disease.

    Optimal Dynamic Prioritization of Scarce COVID-19 Vaccines

    Authors: Jack Hoyt Buckner; Gerardo Hoyt Chowell; Michael R Springborn; Jan-Niklas Salewski; Frederike Winter; Simone Buchtler; Maximilian V Malfertheiner; Matthias Lubnow; Dirk Lunz; Bernhard Graf; Florian Hitzenbichler; Frank Hanses; Hendrik Poeck; Marina Kreutz; Evelyn Orso; Ralph Burkhardt; Tanja Niedermair; Christoph Brochhausen; Andre Gessner; Bernd Salzberger; Matthias Mack; Christine Goffinet; Florian Kurth; Martin Witzenrath; Maria Theresa Völker; Sarah Dorothea Müller; Uwe Gerd Liebert; Naveed Ishaque; Lars Kaderali; Leif Erik Sander; Sven Laudi; Christian Drosten; Roland Eils; Christian Conrad; Ulf Landmesser; Irina Lehmann

    doi:10.1101/2020.09.22.20199174 Date: 2020-09-23 Source: medRxiv

    Multiple promising COVID-19 vaccines are under rapid development, with deployment of the initial supply expected by 2021. Careful design of a vaccine prioritization strategy across socio-demographic groups is an imminent and crucial public policy challenge given that (1) the eventual vaccine supply will be highly constrained for at least the first several months of the vaccination campaign, and (2) there are stark differences in transmission TRANS and severity of impacts from SARS-CoV-2 across groups. Previous experience with vaccine development mid-pandemic offers limited insights for SARS-CoV-2 prioritization: SARS and Zika vaccine development was incomplete when those outbreaks ended and the epidemiology of endemic human influenza viruses differ substantially from that of SARS-CoV-2. We assess the optimal allocation of a limited and dynamic COVID-19 vaccine supply in the U.S. across socio-demographic groups differentiated by age TRANS and essential worker status. The transmission TRANS dynamics are modeled using a compartmental (SEIR) model parameterized to capture our current understanding of the transmission TRANS and epidemiological characteristics of COVID-19, including key sources of group heterogeneity (susceptibility, severity, and contact rates). We investigate tradeoffs between three alternative policy objectives: minimizing infections, years of life lost, or deaths. Moreover, we model dynamic vaccine prioritization policies that respond to changes in the epidemiological status of the population as SARS-CoV-2 continues its march. Because contacts tend to be concentrated within age groups TRANS, there is diminishing marginal returns as vaccination coverage increases in a given group, increasing the group's protective immunity against infection MESHD and mortality. We find that optimal prioritization consistently targets older essential workers. However, depending on the policy objective, younger essential workers are prioritized to minimize infections MESHD or seniors in order to minimize mortality. Optimal prioritization outperforms non-targeted vaccination strategies by up to 18% depending on the outcome optimized. For example, in our baseline model, cumulative mortality decreased on average by 17% (25,000 deaths in the U.S. population) over the course of the outbreak.

    Epidemic Response and Transmission TRANS Dynamics of Coronavirus Disease MESHD (COVID-19) in Khartoum State- Sudan 2020: Study Protocol

    Authors: Mustafa Khidir Mustafa Elnimeiri; Mohanad Kamaleldin Mahmoud Ibrahim; Shahenaz Seifaldeen Mustafa Satti

    doi:10.21203/ Date: 2020-09-19 Source: ResearchSquare

    Background: A novel Coronavirus was identified as severe acute respiratory syndrome Coronavirus 2 MESHD (SARS-CoV-2), and the syndrome of clinical manifestation was named (COVID-19). Consequently, on Jan 30, 2020, the World Health Organization (WHO) declared the outbreak as a pandemic and a public health emergency of international concern. The objectives of this research are to investigate the response of the health system at different levels towards the control of the COVID-19 epidemic and to explore the COVID-19 transmission TRANS dynamics among Sudanese community. Methods: A community and institutional-based cross sectional based study will be conducted in Khartoum State include all the seven localities. The sample size of participant is estimated at 920 using the population formula (n=N/1+ (n*d2)) and considering the response rate. The sample will be drawn using multistage cluster sampling. Data will be collected using interview with key informant and concerned bodies/institutes involved in the response at both the federal and Khartoum State levels. Administered pre-coded, pretested closed ended questionnaire will be developed to collect data from community participants. Data will be managed and analyzed using Statistical Package for Social Sciences version 21. Analysis is mostly univariate descriptive and bi-variate with Chi Square & Fischer Exact tests analysis to find associations between variables of interest.Discussion: This study is expected to evaluate the extent and magnitude of the epidemic response at different levels in addition to the adequacy of the epidemic response. The study participants will be screened to estimate proportion of individuals per age TRANS strata who show sero-positivity for virus infection MESHD, thus it will estimate the percentages of individuals reporting symptoms/signs of infection MESHD and asymptomatic TRANS fraction. The results of this study will strengthen the current interventional approaches of COVID-19 epidemic control and will provide set of database for better planning and implementation of COVID-19 control across the country. It will contribute to in-depth understanding of the COVID-19 transmission TRANS dynamics among Sudanese community and will improve the community awareness about COVID-19.

    In the long shadow of our best intentions: model-based assessment of the consequences of school reopening during the COVID-19 pandemic

    Authors: Kaitlyn E Johnson; Madison Stoddard; Ryan P Nolan; Douglas E White; Natasha S Hochberg; Arijit Chakravarty; Rahul Kumar Anand; Bikash Ranjan Ray; Rajeshwari Subramaniam; Souvik Maitra; 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:10.1101/2020.09.18.20197400 Date: 2020-09-18 Source: medRxiv

    As the United States grapples with the ongoing COVID-19 pandemic, a particularly thorny set of questions surrounds the reopening of K-12 schools and universities. The benefits of in-person learning are numerous, in terms of education quality, mental health, emotional well-being, equity and access to food and shelter. Early reports suggested that children TRANS might have reduced susceptibility to COVID-19, and children TRANS have been shown to experience fewer complications than older adults TRANS. Over the past few months, our understanding of COVID-19 has been further shaped by emerging data, and it is now understood that children TRANS are as susceptible to infection as adults TRANS and have a similar viral load during infection MESHD. While the higher prevalence SERO of asymptomatic TRANS disease among children TRANS makes symptom-based isolation strategies ineffective, asymptomatic TRANS patients do not in fact carry a reduced viral load. Based on this updated understanding of the disease, we have used epidemiological modeling to explore the feasibility and consequences of school reopening in the face of differing rates of COVID-19 prevalence SERO and transmission TRANS. Our findings indicate that, regardless of the initial prevalence SERO of the disease, and in the absence of systematic surveillance testing, most schools in the United States can expect to remain open for 20-60 days. At this point, one or more large disease clusters can be expected to be detected, forcing schools to close again. These disease clusters, in turn, can be expected to propagate through the community, with potentially hundreds to thousands of additional cases resulting from each individual school cluster. Thus, our findings suggest that the debate between the risks to student safety and benefits of in-person learning frames a false dual choice. Given the current circumstances in the United States, the most likely outcome in the late fall HP is that students will be deprived of the benefits of in-person learning while having incurred a significant risk to themselves and their communities.

    Environmental and climatic impact on the infection MESHD and mortality of SARS-CoV-2 in Peru

    Authors: Victor J. Samillan; Diana Flores-Leon; Brian R. Zutta; Eduardo Rojas; Prameela Dinesh; Prakash B G Kumar; Daisy A John; Anita Desai; Ravi Vasanthapuram; Jonathan Flint; Eleazar Eskin; Chongyuan Luo; Shangxin Yang; Omai B Garner; Yi Yin; Joshua S Bloom; Leonid Kruglyak; Jason M Goldstein; Joel M Montgomery; Christina F Spiropoulou

    doi:10.1101/2020.09.16.20196170 Date: 2020-09-18 Source: medRxiv

    The role of the environment and climate in the transmission TRANS and case-fatality rates of SARS-CoV-2 is still being investigated. Elevation and air quality are believed to be significant factors in the current development of the pandemic, but the influence of additional environmental factors remain unclear. In this study, we explored the relationship between the cumulative number of infections MESHD and mortality cases with climate (temperature, precipitation, solar radiation, water vapor pressure, wind), environmental data (elevation, NDVI, PM2.5 and NO2 concentration), and population density in Peru. Using the data from confirmed cases TRANS of infection MESHD from 1287 districts and confirmed cases TRANS of mortality in 479 districts, we used Spearman's correlations to assess the correlation between environmental and climatic factors with cumulative infection cases, cumulative mortality and case-fatality rate. We also explored district cases by the ecozones of coast, sierra, high montane forest and lowland rainforest. Multiple linear regression models indicate elevation, mean solar radiation, air quality, population density and green cover are influential factors in the distribution of infection MESHD and mortality of SARS-CoV-2 in Peru. The case-fatality rate was weakly associated with elevation. Our results also strongly suggest that exposure to poor air quality is a significant factor in the mortality of individuals with SARS-CoV-2 below the age TRANS of 30. We conclude that environmental and climatic factors do play a significant role in the transmission TRANS and case-fatality rates in Peru, however further study is required to see if these relationships are maintained over time.

    Testing, Testing: What SARS-CoV-2 testing services do adults TRANS in the United States actually want?

    Authors: Rebecca Zimba; Sarah Kulkarni; Amanda Berry; William You; Chloe Mirzayi; Drew Westmoreland; Angela Parcesepe; Levi Waldron; Madhura Rane; Shivani Kochhar; McKaylee Robertson; Andrew R Maroko; Christian Grov; Denis Nash; - for the CHASING COVID Cohort Study Team; Daniel R Morales; Fredrik Nyberg; Jose D Posada; Martina Recalde; Elena Roel; Karishma Shah; Nigam Shah; Lisa M Schilling; Vignesh Subbian; David Vizcaya; Lin Zhang; Ying Zhang; Hong Zhu; Li Liu; Peter Rijnbeek; George Hripcsak; Jennifer C.E Lane; Edward Burn; Christian Reich; Marc A Suchard; Talita Duarte-Salles; Krisitn Kosta; Patrick B Ryan; DANIEL PRIETO-ALHAMBRA; Christoph Lange; Georg Laue; Clemes Lier; Matthias Lindner; Georgios Marinos; Robert Markewitz; Jacob Nattermann; Rainer Noth; Peter Pickkers; Klaus F. Rabe; Alina Renz; Christoph Roecken; Jan Rupp; Annika Schaffarzyk; Alexander Scheffold; Jonas Schulte-Schrepping; Domagoj Schunck; Dirk Skowasch; Thomas Ulas; Klaus-Peter Wandinger; Michael Wittig; Johannes Zimmermann; Hauke Busch; Bimba F. Hoyer; Christoph Kaleta; Jan Heyckendorf; Matthijs Kox; Jan Rybniker; Stefan Schreiber; Joachim Schultze; Philip Rosenstiel; - HCA Lung Biological Network; - Deutsche COVID-19 Omics Initiative (DeCOI)

    doi:10.1101/2020.09.15.20195180 Date: 2020-09-18 Source: medRxiv

    Importance: Ascertaining preferences for SARS-CoV-2 testing and incorporating findings into the design and implementation of strategies for delivering testing services may enhance testing uptake and engagement, a prerequisite to reducing onward transmission TRANS. Objective: To determine important drivers of decisions to obtain a SARS-CoV-2 test in the context of increasing community transmission TRANS. Design: A discrete choice experiment (DCE) was used to assess the relative importance of type of SARS-CoV-2 test, specimen type, testing venue, and results turnaround time. Uptake of an optimized testing scenario was simulated relative to the current typical testing scenario of polymerase chain reaction (PCR) via nasopharyngeal (NP) swab in a provider office or urgent care clinic with results in >5 days. Setting: Online survey, embedded in an existing cohort study, conducted during July 30 - September 8, 2020. Participants: Participants (n=4,793) were enrolled in the CHASING COVID Cohort Study, a national longitudinal cohort of adults TRANS >18 years residing in the 50 US states, Washington, DC, Puerto Rico, or Guam. Main Outcome(s) and Measure(s): Relative importance of SARS-CoV-2 testing method attributes, utilities of specific attribute levels, and probability of choosing a testing scenario based on preferences estimated from the DCE, the current typical testing option, or choosing not to test. Results: Turnaround time for test results had the highest relative importance (30.4%), followed by test type (28.3%), specimen type (26.2%), and venue (15.0%). Participants preferred fast results on both past and current infection MESHD and using a noninvasive specimen, preferably collected at home. Simulations suggested that providing immediate or same day test results, providing both PCR and serology, or collecting oral specimens would substantially increase testing uptake over the current typical testing option. Simulated uptake of a hypothetical testing scenario of PCR and serology via a saliva sample at a pharmacy with same day results was 97.7%, compared to 0.6% for the current typical testing scenario, with 1.8% opting for no test. Conclusions and Relevance: Testing strategies that offer both PCR and serology with non-invasive methods and rapid turnaround time would likely have the most uptake and engagement among residents in communities with increasing community transmission TRANS of SARS-CoV-2.

    Epidemiology of SARS-CoV-2 infection MESHD in Karnataka State, South India: Transmission TRANS dynamics of symptomatic vs. asymptomatic TRANS infections

    Authors: Narendra Kumar; Shafeeq K S Hameed; Giridhara R Babu; Manjunatha M Venkataswamy; Prameela Dinesh; Prakash B G Kumar; Daisy A John; Anita Desai; Ravi Vasanthapuram; Jonathan Flint; Eleazar Eskin; Chongyuan Luo; Shangxin Yang; Omai B Garner; Yi Yin; Joshua S Bloom; Leonid Kruglyak; Jason M Goldstein; Joel M Montgomery; Christina F Spiropoulou

    doi:10.1101/2020.09.17.20196501 Date: 2020-09-18 Source: medRxiv

    Background: In this report, we describe the epidemiology of SARS-CoV-2 infection MESHD, specifically examining how the symptomatic persons drove the transmission TRANS in the state of Karnataka, India, during the lockdown phase. Methods: The study included all the cases reported from March 8 to May 31, 2020 in the state. Any person with history of international or domestic travel TRANS from high burden states, those presenting with Influenza-like or Severe Acute Respiratory Illness MESHD and high-risk contacts of COVID19 cases, who were SARS-CoV-2 RT-PCR positive were included. Detailed analysis based on contact TRANS tracing TRANS data available from line-list of the state surveillance unit was performed using cluster analysis software package. Findings: Amongst the 3404 COVID-19 positive cases, 3096 (91%) were asymptomatic TRANS while 308 (9%) were symptomatic. Majority of the asymptomatic TRANS cases were in the age TRANS range of 16-50 years while symptomatic cases were between 31-65 years. Most of those affected were males TRANS. Cluster analysis of 822 cases indicated that the secondary attack rate TRANS, size of the cluster (dispersion) and occurrence of overt clinical illness is significantly higher when the index case in a cluster was symptomatic compared to an asymptomatic TRANS. Interpretation: Our findings indicate that both asymptomatic TRANS and symptomatic SARS-CoV-2 cases transmit the infection MESHD; however, the main driving force behind the spread of infection within the state was significantly higher from symptomatic cases. This has major implications for policies related to testing. Active search for symptomatic cases, subjecting them to testing and treatment should be prioritized for containing the spread of COVID-19.

    Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance

    Authors: Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott; Carlos E. Milla; Angela J. Rogers; Paul L. Bollyky; Marcus VG Lacerda; Pedro M Moraes-Vieira; Helder I Nakaya; Qiao Wang; Hongbin Ji; Youhua Xie; Yihua Sun; Lu Lu; Yunjiao Zhou

    doi:10.1101/2020.09.11.20192492 Date: 2020-09-11 Source: medRxiv

    Background Based on cases and deaths MESHD, transmission TRANS of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence SERO, doubling times between and within rounds and associated reproduction numbers TRANS. We obtained unweighted prevalence SERO estimates by sub- groups: age TRANS, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection MESHD. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic TRANS at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value TRANS of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value TRANS of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence SERO in participants aged TRANS 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence SERO in those aged TRANS 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection MESHD. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission TRANS persisted in England through to mid-summer 2020, the prevalence SERO of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission TRANS at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence SERO.

    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.

    COVID-19 Transmission TRANS Within Danish Households: A Nationwide Study from Lockdown to Reopening

    Authors: Frederik Plesner Lyngse; Carsten Thure Kirkeby; Tariq Halasa; Viggo Andreasen; Robert Leo Skov; Frederik Trier Møller; Tyra Grove Krause; Kåre Mølbak; Zi-wen Guo; Chuang-sheng Hu; Shu-juan Guo; Qing-feng Meng; Yan Ren; Wei Wang; Xiao Yang; Jie Zhou; Xiao-dong Zhao; Hua Li; Sheng-ce Tao; Olivier Elemento; Mirella Salvatore; Giorgio Inghirami

    doi:10.1101/2020.09.09.20191239 Date: 2020-09-09 Source: medRxiv

    Background The Covid-19 pandemic is one of the most serious global public health threats in recent times. Understanding transmission TRANS of SARS-CoV-2 is of utmost importance to be able to respond to outbreaks and take action against spread of the disease TRANS. Transmission within the household TRANS is a concern, especially because infection MESHD control is difficult to apply within the household domain. Methods We used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests, to estimate household transmission TRANS risk and attack rate TRANS. Results We studied the testing dynamics for COVID-19 and found that the day after receiving a positive test result within the household, 35% of potential secondary cases TRANS were tested and 13% of these were positive. After a primary case TRANS in 6,782 households, 82% of potential secondary cases TRANS were tested within 14 days, of which 17% tested positive as secondary cases TRANS, implying an attack rate TRANS of 17%. Among primary cases TRANS, those aged TRANS 0-24 were underrepresented when compared with the total population. We found an approximately linearly increasing relationship between attack rate TRANS and age TRANS. We investigated the transmission risk TRANS from primary cases TRANS by age TRANS, and found an increasing risk with age TRANS of primary cases TRANS for adults TRANS, while the risk seems to decrease with age TRANS for children TRANS. Conclusions Although there is an increasing attack rate TRANS and transmission risk TRANS of SARS-CoV-2 with age TRANS, children TRANS are also able to transmit SARS-CoV-2 within the household.

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MeSH Disease
Human Phenotype

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