Corpus overview


MeSH Disease

Human Phenotype


    displaying 1 - 10 records in total 168
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    COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020

    Authors: Mohamed Elhakim; Saleh Banoita Tourab; Ahmed Zouiten

    doi:10.1101/2020.08.03.20167692 Date: 2020-08-04 Source: medRxiv

    Background: First cases of COVID-19 were reported from Wuhan, China, in December 2019, and it progressed rapidly. On 30 January, WHO declared the new disease MESHD as a PHEIC, then as a Pandemic on 11 March. By mid-March, the virus spread widely; Djibouti was not spared and was hit by the pandemic with the first case detected on 17 March. Djibouti worked with WHO and other partners to develop a preparedness and response plan, and implemented a series of intervention measures. MoH together with its civilian and military partners, closely followed WHO recommended strategy based on four pillars: testing, isolating, early case management, and contact tracing TRANS. From 17 March to 16 May, Djibouti performed the highest per capita tests in Africa and isolated, treated and traced the contacts TRANS of each positive case, which allowed for a rapid control of the epidemic. Methods: COVID-19 data included in this study was collected through MoH Djibouti during the period from 17 March to 16 May 2020. Results: A total of 1,401 confirmed cases TRANS of COVID-19 were included in the study with 4 related deaths MESHD (CFR: 0.3%) and an attack rate TRANS of 0.15%. Males TRANS represented (68.4%) of the cases, with the age group TRANS 31-45 years old (34.2%) as the most affected. Djibouti conducted 17,532 tests, and was considered as a champion for COVID-19 testing in Africa with 18.2 tests per 1000 habitant. All positive cases were isolated, treated and had their contacts traced TRANS, which led to early and proactive diagnosis of cases and in turn yielded up to 95-98% asymptomatic TRANS cases. Recoveries reached 69% of the infected cases with R0 TRANS (0.91). The virus was detected in 4 regions in the country, with the highest percentage in the capital (83%). Conclusion: Djibouti responded to COVID-19 pandemic following an efficient and effective strategy, using a strong collaboration between civilian and military health assets that increased the response capacities of the country. Partnership, coordination, solidarity, proactivity and commitment were the pillars to confront COVID-19 pandemic.

    Therapeutic effectiveness of interferon alpha 2b treatment for COVID-19 patient recovery

    Authors: Ricardo Pereda; Daniel Gonzalez; Hubert Blas Rivero; Juan Carlos Rivero; albadio Perez; Lissette del Rosario Lopez; Natacha Mezquia; Rafael Venegas; Julio Raul Betancourt; Rodolfo Emilio Dominguez

    doi:10.1101/2020.07.28.20157974 Date: 2020-08-04 Source: medRxiv

    Background Effective antiviral treatments are required to contain the ongoing coronavirus disease MESHD 2019 (COVID-19) pandemic. A previous report in 814 patients COVID-19 positive in Cuba provided preliminary therapeutic efficacy evidence with interferon alpha-2b (IFN alpha-2b) from March 11 to April 14, 2020. This study, re-evaluates the contribution of IFN-2b on the evolution of all patients, after 98 days of the epidemic, in a period from March 11 to June 17, 2020. Method A prospective observational study was implemented to monitor a therapeutic intervention with IFN alpha-2b used in the national protocol for COVID-19 attending in Cuba. Were included patients with positive throat swab specimens by real time RT-PCR who gave informed consent and had no contraindications for IFN treatment. Patients received therapy as per the Cuban COVID protocol that included a combination of oral antivirals (lopinavir/ritonavir and chloroquine) with intramuscular or subcutaneous administration of IFN alpha-2b The primary endpoint was the proportion of patients discharged from hospital, secondary was the case TRANS fatality rate and several outcomes related to time variables were also evaluated. Results From March 11th until June 17th, 2295 patients had been confirmed SARS-CoV-2 positive in Cuba, 2165 were treated with Heberon Alpha R and 130 received the approved protocol without IFN. The proportion of fully recovered patients was higher in the IFN-treated compared with non-IFN treated group. Prior IFN treatment decreases the likelihood of intensive care and increases the survival after severe or critical diseases MESHD. The benefits of IFN were significantly supported by time variables analyzed. Conclusions This second report confirm the preliminary evidences from first for the therapeutic effectiveness of IFN alpha-2b for SARS-Cov-2 infection MESHD and postulated that Heberon Alpha R is the main component within the antiviral triad used as a therapeutic intervention in the Cuban protocol COVID-19.

    Household transmission TRANS of SARS-CoV-2: a systematic review and meta-analysis of secondary attack rate TRANS

    Authors: Zachary J. Madewell; Yang Yang; Ira M. Longini Jr.; M. Elizabeth Halloran; Natalie E. Dean

    doi:10.1101/2020.07.29.20164590 Date: 2020-08-01 Source: medRxiv

    Background: Severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) is spread by direct, indirect, or close contact TRANS with infected people via infected respiratory droplets or saliva. Crowded indoor environments with sustained close contact TRANS and conversations are a particularly high-risk setting. Methods: We performed a meta-analysis through July 29, 2020 of SARS-CoV-2 household secondary attack rate TRANS ( SAR TRANS), disaggregating by several covariates (contact type, symptom status, adult TRANS/ child TRANS contacts, contact sex, relationship to index case, index case sex, number of contacts in household TRANS, coronavirus). Findings: We identified 40 relevant published studies that report household secondary transmission TRANS. The estimated overall household SAR TRANS was 18.8% (95% confidence interval [CI]: 15.4%-22.2%), which is higher than previously observed SARs for SARS-CoV and MERS-CoV. We observed that household SARs were significantly higher from symptomatic index cases than asymptomatic TRANS index cases, to adult TRANS contacts than children TRANS contacts, to spouses than other family contacts, and in households TRANS with one contact than households TRANS with three or more contacts. Interpretation: To prevent the spread of SARS-CoV-2, people are being asked to stay at home worldwide. With suspected or confirmed infections TRANS infections MESHD referred to isolate at home, household transmission TRANS will continue to be a significant source of transmission TRANS.

    The relative infectiousness of asymptomatic TRANS SARS-CoV-2 infected persons compared with symptomatic individuals: A rapid scoping review.

    Authors: David Mc Evoy; Conor G McAloon; Aine B Collins; Kevin Hunt; Francis Butler; Andrew W Byrne; Miriam Casey; Ann Barber; John M Griffin; Elizabeth A Lane; Patrick Wall; Simon J More

    doi:10.1101/2020.07.30.20165084 Date: 2020-08-01 Source: medRxiv

    Objectives: The aim of this study was to conduct a scoping review of estimates of the relative infectiousness of asymptomatic TRANS persons infected with SARS-CoV-2 compared with symptomatic individuals. Design: Rapid scoping review of literature available until 8th April 2020. Setting: International studies on the infectiousness of individuals infected with SARS-CoV-2 Participants: Studies were selected for inclusion if they defined asymptomatics TRANS as a separate cohort distinct from pre-symptomatics and if they provided a quantitative measure of the infectiousness of asymptomatics TRANS relative to symptomatics. Primary outcome measures: The relative number of secondary cases TRANS produced by an average primary case TRANS, the relative probability of transmitting infection MESHD upon contact, and the degree of viral shedding. Results: Very few studies reported estimates of relative infectiousness of asymptomatic TRANS compared with symptomatic individuals. Significant differences exist in the definition of infectiousness. Viral shedding studies in general show no difference in shedding levels between symptomatic and asymptomatic TRANS individuals but are likely to be impacted by insufficient statistical power. Two contact tracing TRANS studies provided estimates of 0.7 and 1.0, but differences in approach and definition preclude comparison across the two studies. Finally, two modelling studies suggest a relative infectiousness of around 0.5 but one of these was more reflective of the infectiousness of undocumented rather than asymptomatic TRANS cases. Importantly, one contact tracing TRANS study showing a very low level of infectiousness of asymptomatic TRANS was not included in the analysis at this point due difficulties interpreting the reported findings. Conclusions: The present study highlights the need for additional studies in this area as a matter of urgency. For the purpose of epidemiological modelling, we cautiously suggest that at present, asymptomatics TRANS could be considered to have a degree of infectiousness which is about 0.40-0.70 that of symptomatics. However, it must be stressed that this suggestion comes from a very low evidence base and that estimates exist that are close to zero and close to 1.

    Hybrid capture-based sequencing enables unbiased recovery of SAR TRANS-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants

    Authors: Mingkun Li; Yi Xu; Lu Kang; Zijie Shen; Xufang Li; Weili Wu; Wentai Ma; Chunxiao Fang; Fengxia Yang; Xuan Jiang; Sitang Gong; Li Zhang

    doi:10.1101/2020.07.30.230102 Date: 2020-08-01 Source: bioRxiv

    BackgroundIn response to the current COVID-19 pandemic, it is crucial to understand the origin, transmission TRANS, and evolution of SARS-CoV-2, which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown, partly due to the difficulty of obtaining unbiased genome coverage of SARS-CoV-2 directly from clinical samples. MethodsEighteen time series fecal samples were collected from nine COVID-19 patients during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method with different rounds of hybridization. ResultsBy examining the sequencing depth, genome coverage, and allele frequency change, we demonstrated the impeccable performance SERO of the hybrid capture method in samples with Ct value < 34, as well as significant improvement comparing to direct metatranscriptomic sequencing in samples with lower viral loads. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Meanwhile, we also found that the same mutation showed different frequency changes in different individuals, indicating a strong random drift. Moreover, the evolving of the viral genome demonstrated that the virus was still viable in the gastrointestinal tract during the convalescent period. ConclusionsThe hybrid capture method enables reliable analyses of inter- and intra-host variants of SARS-CoV-2 genome, which changed dramatically in the gastrointestinal tract; its clinical relevance warrants further investigation.

    Transmission TRANS of SARS-CoV-2 following exposure in school settings: experience from two Helsinki area exposure incidents.

    Authors: Timothee Dub; Elina Erra; Lotta Hagberg; Emmi Sarvikivi; Camilla Virta; Asko Jarvinen; Pamela Osterlund; Niina Ikonen; Anu Haveri; Merit Melin; Timo J Lukkarinen; Hanna Nohynek

    doi:10.1101/2020.07.20.20156018 Date: 2020-07-30 Source: medRxiv

    Background: The role of children TRANS in SARS-CoV-2 transmission TRANS is unclear. We investigated two COVID-19 school exposure incidents in the Helsinki area. Methods: We conducted two retrospective cohort studies after schools exposures, with a household transmission TRANS extension. We defined a case as an exposed person with either a positive RT-PCR, or positive microneutralisation testing (MNT) as confirmation of SARS-CoV-2 nucleoprotein IgG antibodies SERO detection via fluorescent microsphere immunoassay SERO (FMIA). We recruited close school contacts and families of school cases, calculated attack rates TRANS (AR) on school level and families, and identified transmission chains TRANS. Findings: In incident A, the index was a pupil. Participation rate was 74% (89/121), and no cases were identified. In incident B, the index was a member of school personnel. Participation rate was 81% (51/63). AR was 16% (8/51): 6 pupils and 1 member of school personnel were MNT and FMIA positive; 1 pupil had a positive RT-PCR, but negative serology samples. We visited all school cases' families (n=8). The AR among close household contacts TRANS was 42% (9/20 in 3/8 families) but other plausible sources were always reported. At three months post-exposure, 6/8 school cases were re-sampled and still MNT positive. Interpretation: When the index was a child TRANS, no school transmission TRANS was identified, while the occurrence of an adult TRANS case led to a 16% AR. Further cases were evidenced in 3 families, but other transmission chains TRANS were plausible. It is likely that transmission TRANS from children TRANS to adults TRANS is limited. Funding: The Finnish Institute for Health and Welfare funded this study.

    The COVID-19 Pandemic in Francophone West Africa: From the First Cases to Responses in Seven Countries

    Authors: Emmanuel Bonnet; oriane Bodson; Fréderic Le Marcis; Adama Faye; Emmanuel Sambieni; Florence Fournet; Florence Boyer; Abdourahmane Coulibaly; Kadidiatou Kadio; Fatoumata Binetou Diongue; Valery Ridde

    doi:10.21203/ Date: 2020-07-29 Source: ResearchSquare

    Background: In early March 2020, the COVID-19 pandemic hit West Africa. Countries in the region quickly set up crisis management committees and organised drastic measures to stem the spread of the coronavirus. The objective of this article is to analyse the epidemiological evolution of COVID-19 in seven Francophone West African countries (Benin, Burkina Faso, Côte d'Ivoire, Guinea, Mali, Niger, Senegal) as well as the public health measures decided upon during the first four months of the pandemic.  Methods: Our method is based on quantitative and qualitative data from the pooling of information from a COVID-19 data platform and collected by a network of interdisciplinary collaborators present in the seven countries. Descriptive and spatial analyses of quantitative epidemiological data and content analyses of qualitative data on public measures and management committees were performed. Results: Attack rates TRANS for COVID-19 range from less than 10 per 100,000 inhabitants (Benin) to more than 45 per 100,000 inhabitants (Guinea). The spatio-temporal analysis shows three phases of incidence clusters. By the end of June 2020, case numbers had plateaued in some countries (Burkina Faso, Niger, Mali) while others continued to see the number of infections MESHD increasing (Benin, Côte d'Ivoire, Guinea, Senegal). The countries all reacted quickly to the crisis, in some cases before the first reported infection MESHD, and implemented public measures in a relatively homogeneous manner. None of the countries implemented country-wide lockdowns, but in some cases implemented partial or local containment measures. At the end of June 2020, countries began to lift certain restrictive measures, sometimes under pressure from the general population or from certain economic sectors. All the countries have adopted response plans and organized multiple crisis management committees, although their content and functioning have not always been transparent or easy to understand. Conclusion: Much research remains to be done in West Africa. It will be necessary to better understand the dynamics of the pandemic, which appears to be largely under control, as well as the effectiveness and implementation of the state responses, which have been rapidly formulated.

    High Rate of SARS-CoV-2 Transmission TRANS due to Choir Practice in France at the Beginning of the COVID-19 Pandemic

    Authors: Nathalie CHARLOTTE

    doi:10.1101/2020.07.19.20145326 Date: 2020-07-25 Source: medRxiv

    Background: There has been little focus on the individual risk of acquiring COVID-19 related to choir practice. Methods: We report the case of a high transmission TRANS rate of SARS-CoV-2 linked to an indoor choir rehearsal in France in March 2020 at the beginning of the COVID-19 pandemic. Results: A total of 27 participants, including 25 male TRANS singers, a conductor and an accompanist attended a choir practice on March 12, 2020. The practice was indoor and took place in a non-ventilated space of 45 m2. No choir member reported having been symptomatic for COVID-19 between March 2 and March 12.The mean age TRANS of the participants was 66.9 (range 35-86) years. 70% of the participants (19 of 27) were diagnosed with COVID-19 from 1 to 12 days after the rehearsal with a median of 5.1 days. 36% of the cases needed a hospitalization (7/19), and 21% (4/19) were admitted to an ICU. The index cases were possibly multiple. Discussion: The choir practice was planned in March 2020 at a period when the number of new cases of COVID-19 began to grow exponentially in France because SARS-CoV-2 was actively circulating. The secondary attack rate TRANS (70%) was much higher than it is described within households (10-20%) and among close contacts TRANS made outside households (0-5%). Singing might have contributed to enhance SARS-CoV-2 person-to-person transmission TRANS through emission of droplets and aerosolization in a closed non ventilated space with a relative high number of people including multiple pre-symptomatic suspected index cases. Conclusion: Indoor choir practice should be suspended during SARS-CoV-2 outbreaks. Further studies are necessary to test the spread of the virus by the act of singing. As the benefits of the barrier measures and social distancing are known to be effective in terms of a reduction in the incidence of the COVID-19, experts recommendations concerning the resuming of choir practice are necessary.

    Model-free estimation of COVID-19 transmission TRANS dynamics from a complete outbreak

    Authors: Alex James; Michael J Plank; Shaun Hendy; Rachelle N Binny; Audrey Lustig; Nic Steyn

    doi:10.1101/2020.07.21.20159335 Date: 2020-07-24 Source: medRxiv

    Background New Zealand had 1499 cases of COVID-19 before eliminating transmission TRANS of the virus. Extensive contract tracing TRANS during the outbreak has resulted in a dataset of epidemiologically linked cases. This data contains useful information about the transmission TRANS dynamics of the virus, its dependence on factors such as age TRANS, and its response to different control measures. Method We use Monte-Carlo network construction techniques to provide an estimate of the number of secondary cases TRANS for every individual infected during the outbreak. We then apply standard statistical techniques to quantify differences between groups of individuals. Findings Children TRANS under 10 years old are significantly under-represented in the case data. Children TRANS infected fewer people on average and had a lower secondary attack rate TRANS in comparison to adults TRANS and the elderly TRANS. Imported cases infected fewer people on average and had a lower secondary attack rate TRANS than domestically acquired cases. Superspreading is a significant contributor to the epidemic dynamics, with 20% of cases among adults TRANS responsible for 65-85% of transmission TRANS. Asymptomatic TRANS cases infected fewer individuals than clinical cases. Serial intervals TRANS are approximately normally distributed (=5.0 days, {sigma}=5.7 days). Early isolation and quarantine of cases reduced secondary transmission TRANS rates. Interpretation Border controls and strong social distancing measures, particularly when targeted at superspreading, play a significant role in reducing the spread of COVID-19. Funding Te P[u]naha Matatini, the New Zealand Centre of Research Excellence in complex systems. New Zealand Ministry of Business, Innovation and Employment.

    Evaluating Scenarios for School Reopening under COVID19

    Authors: Pinar Keskinocak; John Asplund; Nicoleta Serban; Buse Eylul Oruc Aglar

    doi:10.1101/2020.07.22.20160036 Date: 2020-07-24 Source: medRxiv

    Thousands of school systems have been struggling with the decisions about how to safely and effectively deliver education during the fall HP semester of 2020, amid the COVID19 pandemic. The objective of this study is to evaluate the public health impact of reopening schools on the spread of COVID19. An agent-based simulation model was adapted and used to project the number of infections MESHD and deaths MESHD under multiple school reopening dates and scenarios, including different cohorts receiving in-person instruction on alternating days, only younger children TRANS returning to in-person instruction, regular schedule (all students receiving in-person instruction), and school closure (all students receiving online instruction). The study period was February 18th-November 24th, 2020 and the state of Georgia was used as a case study. Across all scenarios, the number of COVID19-related deaths MESHD ranged from approximately 17 to 22 thousand during the study period, and on the peak day, the number of new infections MESHD ranged from 43 to 68 thousand. An alternating school day schedule performed: (i) almost as well as keeping schools closed, with the infection MESHD attack rate TRANS ranging from 38.5% to 39.8% compared to that of 37.7% under school closure; (ii) slightly better than only allowing children TRANS 10 years or younger to return to in-person instruction. Delaying the reopening of schools had a minimal impact on reducing infections MESHD and deaths MESHD under most scenarios.

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MeSH Disease
Human Phenotype

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