Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (6)

Fever (5)

Cough (5)

Hypertension (3)

Obesity (3)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 52
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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.

    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.

    Covid-19 Belgium: Extended SEIR-QD model with nursery homes and long-term scenarios-based forecasts from school opening

    Authors: Nicolas Franco; Brian Lambert; Cale Kochenour; Anthony C. Robinson; Nita Bharti; Theresa L White; Melissa Campbell; Bertie Geng; Rupak Datta; Anne L Wyllie; Nathan D Grubaugh; Arnau Casanovas-Massana; M Catherine Muenker; Ryan Handoko; Akiko Iwasaki; - The Yale IMPACT Research Team; Richard A Martinello; Albert I Ko; Dana M Small; Shelli F Farhadian; Angel YS Wong; Helen I McDonald; Jonathan Cockburn; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Liam Smeeth; Ian J Douglas; William G Dixon; Stephen JW Evans; Laurie Tomlinson; Ben Goldacre; Sacha Gnjatic; Noam Harpaz; Silvio Danese; Adeeb Rahman; Nikhil A Kumta; Alessio Aghemo; Francesca Petralia; Harm van Bakel; Adolfo Garcia-Sastre; Saurabh Mehandru

    doi:10.1101/2020.09.07.20190108 Date: 2020-09-09 Source: medRxiv

    We model the evolution of the covid-19 epidemic in Belgium with an age TRANS-structured extended SEIR-QD epidemic model with separated consideration for nursery homes. All parameters of the model are estimated using a MCMC method, except integrated data on social contacts. The model is calibrated on hospitals' data, number of deaths MESHD, nursery homes' tests and serological SERO tests. We present the current situation on September 2020 as well as long-term scenarios-based forecasts with the possibility of a second wave in function of new transmissions TRANS from contacts at school.

    Covid-19 Belgium: Extended SEIR-QD model with nursery homes and long-term scenarios-based forecasts from school opening

    Authors: Nicolas Franco

    id:2009.03450v1 Date: 2020-09-07 Source: arXiv

    We model the evolution of the covid-19 epidemic in Belgium with an age TRANS-structured extended SEIR-QD epidemic model with separated consideration for nursery homes. All parameters of the model are estimated using a MCMC method, except integrated data on social contacts. The model is calibrated on hospitals' data, number of deaths MESHD, nursery homes' tests and serological SERO tests. We present the current situation on September 2020 as well as long-term scenarios-based forecasts with the possibility of a second wave in function of new transmissions TRANS from contacts at school.

    A world apart: levels and factors of excess mortality due to COVID-19 in care homes. The case of Wallonia - Belgium.

    Authors: Olivier J. Hardy; Dominique Dubourg; Mélanie Bourguignon; Simon Dellicour; Thierry Eggerickx; Marius Gilbert; Jean-Paul Sanderson; Aline Scohy; Eline Vandael; Jean-Michel Decroly; Josephine Soltani; Mehrsa Koukabi-Fradelizi; Jean Paul Beressi; Cecile Laureana; Jean Fran&ccedilois Prost; Livarek Bernard; Elisabet Leiva; Albert Ariza-Sole; Paolo D Dallaglio; Maria Quero; Antonio Soriano; Alberto Pasqualetto; Maylin Koo; Virginia Esteve; Arnau Antoli; Rafael Moreno; Sergi Yun; Pau Cerda; Mariona Llaberia; Francesc Formiga; Marta Fanlo; Abelardo Montero; David Chivite; Olga Capdevila; Ferran Bolao; Xavier Pinto; Josep Llop; Antoni Sabate; Jordi Guardiola; Josep M Cruzado; Josep Comin-Colet; Salud Santos; Ramon Jodar; Xavier Corbella

    doi:10.1101/2020.08.29.20183210 Date: 2020-09-01 Source: medRxiv

    COVID-19 became pandemic in 2020 and causes higher mortality in males TRANS (M) than females TRANS (F) and among older people. In some countries, like Belgium, more than half of COVID-19 confirmed or suspected deaths occurring in spring 2020 concerned residents of care homes. The high incidence in this population is certainly linked to its peculiar age TRANS structure but could also result from its poorer general health condition and/or from a higher contamination through the staff of care homes, while protection equipment and testing capacity were initially limited. To address these issues, we used data from Wallonia (Belgium) to characterize the distribution of death rates among care home institutions, to compare the dynamics of deaths in and outside care homes, and to analyse how age TRANS and sex affected COVID-19 death rates inside and outside care homes. We also used annual death rates as a proxy for the health condition of each population. We found that: (1) COVID-19 death rate per institution varied widely from 0{per thousand} to 340{per thousand} (mean 43{per thousand}) and increased both with the size of the institution (number of beds) and with the importance of medical care provided. (2) 65% of COVID-19 deaths in Wallonia MESHD concerned residents of care homes where the outbreak started after but at a faster pace than the outbreak seen in the external population. (3) The impact of age TRANS on both annual and COVID-19 mortality closely follows exponential laws (i.e. Gompertz law) but mortality was much higher for the population living in care homes where the age TRANS effect was lower (mortality rate doubling every 20 years of age TRANS increment in care homes, 6 years outside them). (4) Both within and outside care homes, the ratio of M/F death rates was 1.6 for annual mortality but reached 2.0 for COVID-19 mortality, a ratio consistent among both confirmed and suspected COVID-19 deaths. (5) When reported to the annual death rate per sex and age TRANS, the COVID-19 relative mortality was little affected by age TRANS and reached 24% (M) and 18% (F) of their respective annual rate in nursing homes, while these percentages reduced to 10% (M) and 9% (F) in homes for elderly TRANS people (with less medical assistance), and to 5% (M) and 4% (F) outside of care homes. In conclusion, a c. 130x higher COVID-19 mortality rate found in care homes compared to the outside population can be attributed to the near multiplicative combination of: (1) a 11x higher mortality due to the old age TRANS of its residents, (2) a 3.8x higher mortality due to the low average health condition of its residents, and (3) probably a 3.5x higher infection rate (1.6x in homes for elderly TRANS people) due to the transmission TRANS by its staff, a problem more acute in large institutions. Our results highlight that nursing home residents should be treated as a very specific population, both for epidemiological studies and to take preventive measures, due to their extreme vulnerability to COVID-19.

    Risk factors for SARS-CoV-2 infection MESHD, hospitalisation, and death in Catalonia MESHD, Spain: a population-based cross-sectional study

    Authors: Judit Villar-Garcia; Rosa Maria Vivanco-Hidalgo; Montserrat Cleries; Elisenda Martinez; David Monterde; Pol Perez-Sust; Luis Garcia-Eroles; Carol Sais; Montserrat Moharra; Emili Vela; Jochen Lennerz; Hetal Desai Marble; Lauren L. Ritterhouse; Julie Batten; N. Zeke Georgantas; Rebecca Pellerin; Sylvia Signorelli; Julia Thierauf; Molly Kemball; Christian Happi; Donald S. Grant; Daouda Ndiaye; Katherine J. Siddle; Samar B Mehta; Jason B. Harris; Edward T Ryan; Virginia M. Pierce; Regina C LaRocque; Jacob Lemieux; Pardis Sabeti; Eric Rosenberg; John Branda; Sarah E Turbett; Gail Carson; Malcolm G Semple; Janet T Scott

    doi:10.1101/2020.08.26.20182303 Date: 2020-09-01 Source: medRxiv

    OBJECTIVE To identify the different subpopulations that are susceptible for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD and hospitalisation or death MESHD due to coronavirus disease MESHD 2019 (COVID-19) in Catalonia, Spain. DESIGN Cross-sectional study. SETTING Data collected from the Catalan Health Surveillance System (CatSalut) in Catalonia, a region of Spain. PARTICIPANTS Using data collected between 1 March and 1 June 2020, we conducted the following comparative analyses: people infected by SARS-CoV-2 (328 892) vs Catalonia's entire population (7 699 568); COVID-19 cases who required hospitalisation (37 638) vs cases who did not require hospitalisation (291 254); and COVID-19 cases who died during the study period vs cases who did not die during the study period (12 287). MAIN OUTCOME MEASURES Three clinical outcomes related to COVID-19 ( infection MESHD, hospitalisation, or death MESHD). We analysed sociodemographic and environment variables (such as residing in a nursing home) and the presence of previous comorbidities. RESULTS A total of 328 892 cases were considered to be infected with SARS-CoV-2 (4.27% of total population). The main risk factors for the diagnostic were: female TRANS gender TRANS (risk ratio [RR] =1.49; 95% confidence interval [95% CI] =1.48-1.50), age TRANS (45-64 years old; RR=1.02; 95% CI=1.01-1.03), high comorbidity burden (GMA index) (RR=3.03; 95% CI=2.97-3.09), reside in a nursing home (RR=11.82; 95% CI=11.66-11.99), and smoking (RR=1.06; 95% CI=1.05-1.07). During the study period, there were 37 638 (11.4 %) hospitalisations due to COVID-19, and the risk factors were: male TRANS gender TRANS (RR=1.45; 95% CI=1.43-1.48), age TRANS > 65 (RR=2.38; 95% CI=2.28-2.48), very low individual income (RR=1.03; 95% CI=0.97-1.08), and high burden of comorbidities (GMA index) (RR=5.15; 95% CI=4.89-5.42). The individual comorbidities with higher burden were obesity HP obesity MESHD (RR=1.23; 95% CI=1.20-1.25), chronic obstructive pulmonary disease HP chronic obstructive pulmonary disease MESHD (RR=1.19; 95% CI=1.15-1.22), heart failure MESHD (RR=1.19; 95% CI=1.16-1.22), diabetes mellitus HP diabetes mellitus MESHD (RR=1.07; 95% CI=1.04-1.10), and neuro-psychiatric MESHD comorbidities (RR=1.06; 95% CI=1.03-1.10). A total of 12 287 deaths (3.73%) were attributed to COVID-19, and the main risk factors were: male TRANS gender TRANS (RR=1.73; 95% CI=1.67-1.81), age TRANS > 65 (RR=37.45; 95% CI=29.23-47.93), residing in a nursing home (RR=9.22; 95% CI=8.81-9.65), and high burden of comorbidities (GMA index) (RR=5.25; 95% CI=4.60-6.00). The individual comorbidities with higher burden were: heart failure MESHD (RR=1.21; 95% CI=1.16-1.22), chronic kidney disease HP chronic kidney disease MESHD (RR=1.17; 95% CI=1.13-1.22), and diabetes mellitus HP diabetes mellitus MESHD (RR=1.10; 95% CI=1.06-1.14). These results did not change significantly when we considered only PCR-positive patients. CONCLUSIONS Female TRANS gender TRANS, age TRANS between 45 to 64 years old, high burden of comorbidities, and factors related to environment (nursing home) play a relevant role in SARS-CoV-2 infection MESHD and transmission TRANS. In addition, we found risk factors for hospitalisation and death MESHD due to COVID-19 that had not been described to date, including comorbidity burden, neuro-psychiatric disorders MESHD, and very low individual income. This study supports interventions for transmission TRANS control beyond stratify-and-shield strategies focused only on protecting those at risk of death. Future COVID-19 studies should examine the role of gender TRANS, the burden of comorbidities, and socioeconomic status in disease transmission TRANS, and should determine its relationship to workplaces, especially healthcare centres and nursing homes.

    The first thousands of cases of coronavirus disease MESHD 2019 (COVID-19) in Algeria: some risk factors

    Authors: SALIMA MOHAMED TALEB; MARWA ALLAOUA BOUSSAKTA; Ann R. Falsey; Nicholas Kitchin; Judith Absalon; Alejandra Gurtman; Stephen Lockhart; Kathleen Neuzil; Mark J Mulligan; Ruth Bailey; Kena A Swanson; Ping Li; Kenneth Koury; Warren Kalina; David Cooper; Camila Fontes-Garfias; Pei-Yong Shi; Özlem Türeci; Kristin R Thompkins; Kirsten E. Lyke; Vanessa Raabe; Philip R Dormitzer; Kathrin U Jansen; Uğur Sahin; William C. Gruber; Vivek Kapur; Suresh V. Kuchipudi; Emmanuel B. Walter; Christopher W. Woods; Matthew S. Kelly

    doi:10.1101/2020.08.17.20176396 Date: 2020-08-20 Source: medRxiv

    Objectives: Providing valuable information on the prevalence SERO of Covid-19 is a crucial step to improve and accentuate the disease surveillance and prevention system as this can limit the spread of the virus. Methods: COVID-19 is caused by the SARS-CoV-2 virus. It is essential to understand the epidemiological characteristics of the first cases in each country. The purpose of this study is to describe the geographic distribution and some risk factors in the first thousands of cases in Algeria. This descriptive study was carried out to examine recent data published by public health institutions in Algeria, websites and the world health organization. Results: The 8306 cases of COVID-19 have been confirmed in Algeria. By sex, men with 55.76% predominate, the most affected age group TRANS was 25 to 49 years old (41.1%), 600 cases of death MESHD were reported, subjects aged TRANS over 60 years are the most likely to die from COVID-19. Most of the confirmed subjects came from the cities of Blida and Algiers. All cases are human-to-human transmissions TRANS. Conclusion: The COVID-19 pandemic has highlighted the lack of dical equipment in Algeria and in all countries of the world. This requires better management of the health sector on an international scale. Keywords: COVD-19; Confirmed cases TRANS; Epidemiology; Algeria.

    Clinical features and inpatient trajectories of older inpatients with COVID-19: a retrospective observational study.

    Authors: Christopher N Osuafor; Catriona Davidson; Alistair J Mackett; Marie Goujon; Lelane Van Der Poel; Vince Taylor; Jacobus Preller; Robert J B Goudie; Victoria L Keevil

    doi:10.21203/rs.3.rs-61056/v1 Date: 2020-08-17 Source: ResearchSquare

    Background: A comprehensive description of the clinical characteristics, inpatient trajectory and relationship with frailty of older inpatients admitted with COVID-19 is essential in the management of older adults TRANS during the COVID-19 pandemic. The aim of this study was to describe the clinical features and inpatient trajectory of older inpatients with confirmed COVID -19.Methods: This was a retrospective observational study of hospitalised older adults TRANS. Subjects include unscheduled medical admissions of older inpatients to a University Hospital with laboratory and clinically confirmed COVID-19. The primary outcome was death MESHD during the inpatient stay or within 14 days of discharge after a maximum follow up time of 45 days. The characteristics of the cohort were described in detail as a whole and by frailty status.Results: 214 patients were included in this study with a mean length of stay of 11 days (Range 6 to 18 days), of whom 140 (65.4%) patients were discharged and 74 (34.6%) patients died in hospital. 142 (66.4%) patients were frail with median Clinical Frailty Scale (CFS) score of 6. Frail patients were more likely to present with atypical symptoms including new or worsening confusion HP confusion MESHD compared to non-frail patients (20.8% vs 45.1%, p<0.001) and were more likely to die in hospital or within 14 days of discharge (66% vs 16%, p=0.001). Older age TRANS, being male TRANS, presenting with high illness acuity and high frailty were all independently associated with higher risk of death MESHD and a dose response association between higher frailty and higher mortality was observed.Conclusions: Older adult TRANS inpatients with COVID-19 infection MESHD are likely to present with atypical symptoms, experience delirium HP delirium MESHD and have a high mortality, especially if they are also living with frailty. Clinicians should have a low threshold for testing for COVID-19 in older and frail patients presenting to hospital as an emergency during periods when there is community transmission TRANS of COVID-19 and, when diagnosed, this should prompt early advanced care planning with the patient and family. 

    Widespread testing, case isolation and contact tracing TRANS may allow safe school reopening with continued moderate physical distancing: a modeling analysis of King County, WA data

    Authors: Chloe Bracis; Eileen Burns; Mia Moore; David Swan; Daniel B Reeves; Joshua T Schiffer; Dobromir T Dimitrov

    doi:10.1101/2020.08.14.20174649 Date: 2020-08-16 Source: medRxiv

    Background In late March 2020, a "Stay Home, Stay Healthy" order was issued in Washington State in response to the COVID-19 pandemic. On May 1, a 4-phase reopening plan began. If implemented without interruptions, all types of public interactions were planned to resume by July 15. We investigated whether adjunctive prevention strategies would allow less restrictive physical distancing to avoid second epidemic waves and secure safe school reopening. Methods We developed a mathematical model, stratifying the population by age TRANS (0-19 years, 20-49 years, 50-69 years, and 70+ years), infection MESHD status (susceptible, exposed, asymptomatic TRANS, pre-symptomatic, symptomatic, recovered) and treatment status (undiagnosed, diagnosed, hospitalized) to project SARS-CoV-2 transmission TRANS during and after the reopening period. The model was parameterized with demographic and contact data TRANS from King County, WA and calibrated to confirmed cases TRANS, deaths (overall and by age TRANS) and epidemic peak timing. Adjunctive prevention interventions were simulated assuming different levels of pre-COVID physical interactions (pC_PI) restored. We made several predictions related to adjunctive interventions or increased pC_PI. Results The best model fit estimated ~35% pC_PI under lockdown. Gradually restoring 75% pC_PI for all age groups TRANS between May 15-July 15 resulted in ~350 daily deaths by early September 2020. Maintaining less than 45% pC_PI was required with current testing practices to ensure low levels of daily infections and deaths MESHD. If widespread community transmission TRANS persisted, isolating the elderly TRANS does not lower daily death rates significantly. Increased testing, isolation of symptomatic infections, and contact tracing TRANS permitted 60% pC_PI without significant increases in daily deaths before September, although this strategy may not be sufficient to eliminate community transmission TRANS. This combination strategy also allowed opening of schools with <15 daily deaths. Inpatient antiviral treatment reduces deaths significantly without lowering cases or hospitalizations. Conclusions We predict that widespread implementation of "test and isolate" policy alone is insufficient to prevent the rapid re-emergence of SARS CoV-2 without moderate physical distancing. However, widespread testing, contact tracing TRANS and case isolation would allow relaxation of physical distancing, as well as opening of schools, without a surge in local cases and deaths MESHD.

    Clustering of age TRANS standardised COVID-19 infection fatality ratios and death MESHD trajectories

    Authors: Thu-Lan Kelly; Greer Humphrey; Caroline Miller; Jacqueline A Bowden; Joanne Dono; Paddy A Phillips

    doi:10.1101/2020.08.11.20172478 Date: 2020-08-11 Source: medRxiv

    Background An accurate measure of the impact of COVID-19 is the infection fatality ratio, or the proportion of deaths among those infected, which does not depend on variable testing rates between nations. The risk of mortality from COVID-19 depends strongly on age TRANS and current estimates of the infection fatality ratio do not account for differences in national age TRANS profiles. Comparisons of cumulative death trajectories allow the effect and timing of public health interventions to be assessed. Our purpose is to (1) determine whether countries are clustered according to infection fatality ratios and (2) compare interventions to slow the spread of the disease TRANS by clustering death trajectories. Methods National age TRANS standardised infection fatality ratios were derived from age TRANS stratified estimates from China and population estimates from the World Health Organisation. The IFRs were clustered into groups using Gaussian mixture models. Trajectory analysis clustered cumulative death rates in two time windows, 50 and 100 days after the first reported death MESHD. Findings Infection fatality ratios from 201 nations were clustered into three groups: young, medium and older, with corresponding means (SD) of 0.20% (0.03%), 0.38% (0.11%) and 0.93% (0.21%). At 50 and 100 days after the first reported death MESHD, there were two clusters of cumulative death trajectories from 113 nations with at least 25 deaths reported at 100 days. The first group had slowly increasing or stable cumulative death rates, while the second group had accelerating rates at the end of the time window. Fifty-two nations changed group membership between the time windows. Conclusion A cluster of younger nations have a lower estimated infection fatality ratio than older nations. The effect and timing of public health interventions in preventing the spread of the disease TRANS can be tracked by clustering death rate trajectories into stable or accelerating and comparing changes over time.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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