Corpus overview


MeSH Disease

Human Phenotype


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    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.

    Social Network Analysis of COVID-19 Transmission TRANS in Karnataka, India

    Authors: Sakranaik Saraswathi; Amita Mukhopadhyay; Hemant Shah; T S Ranganath; Sabrina Di Stefano; Valeria Burgos; Jorge Federico Sinner; Marcelo Raul Risk; Eduardo San Roman; Marcos Jose Las Heras; Eduardo Marquez-Garcia; Edda Sciutto; Jose Moreno-Rodriguez; Jose Omar Barreto-Rodriguez; Hazel Vazquez-Rojas; Gustavo Ivan Centeno-Saenz; Nestor Alvarado-Pena; Citlaltepetl Salinas-Lara; Carlos Sanchez-Garibay; Gabriela Hernandez-Molina; Criselda Mendoza-Milla; Andrea Dominguez; Julio Granados; Lula Mena-Hernandez; Luis Angel Perez-Buenfil; Guillermo Dominguez-Cheritt; Carlos Cabello-Gutierrez; Cesar Luna-Rivero; Jorge Salas-Hernandez; Patricio Santilla-Doherty; Justino Regalado; Angelica Hernandez-Martinez; Lorena Orozco; Ethel A. Garcia-Latorre; Carmen M. Hernandez-Cardenas; Shabaana A. Khader; Albert Zlotnik; Joaquin Zuniga

    doi:10.1101/2020.08.11.20172734 Date: 2020-08-14 Source: medRxiv

    We used social network analysis (SNA) to study the novel coronavirus (COVID-19) outbreak in Karnataka, India, and assess the potential of SNA as a tool for outbreak monitoring and control. We analyzed contact tracing TRANS data of 1147 Covid-19 positive cases (mean age TRANS 34.91 years, 61.99% aged TRANS 11-40, 742 males TRANS), anonymized and made public by the government. We used software tools Cytoscape and Gephi to create SNA graphics and determine network attributes of nodes (cases) and edges (directed links, determined by contact tracing TRANS, from source to target patients). Outdegree was 1-47 for 199 (17.35%) nodes, and betweenness 0.5-87 for 89 (7.76%) nodes. Men had higher mean outdegree and women, higher betweenness. Delhi was the exogenous source of 17.44% cases. Bangalore city had the highest caseload in the state (229, 20%), but comparatively low cluster formation. Thirty-four (2.96%) super-spreaders (outdegree[≥]5) caused 60% of the transmissions TRANS. Real-time social network visualization can allow healthcare administrators to flag evolving hotspots and pinpoint key actors in transmission TRANS. Prioritizing these areas and individuals for rigorous containment could help minimize resource outlay and potentially achieve a significant reduction in COVID-19 transmission TRANS.

    Social Behaviors Associated with a Positive COVID-19 Test Result

    Authors: Sidra Speaker; Christine Marie Doherty; Elizabeth R Pfoh; Aaron Dunn; Bryan Hair; Victoria Shaker; Lynn Daboul; Michael B Rothberg

    doi:10.1101/2020.08.04.20168450 Date: 2020-08-06 Source: medRxiv

    Objective: To compare behaviors of individuals who tested positive for COVID-19 relative to non-infected individuals. Methods: We sent COVID positive cases and age TRANS/ gender TRANS matched controls a survey regarding their social behaviors via MyChart (online patient portal). We called cases if they did not complete the electronic survey within two days. Data was collected from May-June 2020. Survey responses for cases without a close contact TRANS and controls were compared using Pearson chi-square or Fishers Exact tests as appropriate. Results: A total of 339 participants completed the survey (113 cases, 226 controls); 45 (40%) cases had known contact with COVID-19. Cases were more likely to have recently traveled TRANS (4% vs. 0%, p=0.01) or to work outside the home (40% vs. 25%, p=0.02). There was no difference in the rates of attending private or public gatherings, mask/glove use, hand-washing, cleaning surfaces and cleaning mail/groceries between cases and controls. Conclusions: Sixty percent of cases had no known contact with COVID-19, indicating ongoing community transmission TRANS and underlining the importance of contact tracing TRANS. The greater percentage of cases who work outside the home provides further evidence for social distancing.

    Epidemiological Characteristics of COVID-19 and Efforts to Prevent Community Transmission TRANS: The Sri Lankan Experience

    Authors: Manjula Kariyawasam; Sashimali Wickramasinghe; Samitha Ginige; Sudath Samaraweera; Paba Palihawadana; Thilanga Ruwanpathirana; Chintha Jayasinghe; Hathshya Munasingha; Alinda Perera; Thiraj Haputhanthri; Deepa Gamage

    doi:10.21203/ Date: 2020-08-05 Source: ResearchSquare

    Background – With the onset of COVID-19 pandemic, the government of Sri Lanka took proactive measures to prevent a community outbreak in the country. This paper describes the measures taken by the government in the initial stages to contain the virus, along with the epidemiological characteristics of the first 200 laboratory confirmed COVID-19 patients.Methods – Telephone interviews were conducted for first 200 consecutive patients diagnosed with COVID-19, after obtaining informed verbal consent. Descriptive data are presented as binary variables and in frequency distribution tables.Results- From the diagnosis of the first patient, 76 days elapsed for the first 200 patients to be diagnosed. Majority were males TRANS in the 40-49 age group TRANS. There were three foreign nationals, while others were Sri Lankans. Among the Sri Lankans, 81 (41.1%) had an overseas travel TRANS history. Following implementation of the cohort quarantine concept, 47% of the overseas returnees were reported from quarantine centres. Over two-thirds of the patients presented with symptoms (n=137, 68.5%) and the most common symptoms were fever HP fever MESHD, cough HP cough MESHD and sore throat. The case fatality rate for the sample was 3.5%. out of the 200 patients, 103 (51.5%) were primary patients, while 92 (46%) were secondary patients. The source of exposure could not be determined for five patients. Conclusions – Due to measures instigated by the government, such as cohort quarantining, extensive contact tracing TRANS and testing of close contacts TRANS, Sri Lanka was able to prevent a wide spread community outbreak of COVID-19.

    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.

    Knowledge, Attitudes, and Practices of Medical Interns Toward COVID-19 in Saudi Arabia: A Cross-Sectional Survey, April-May 2020

    Authors: Sultan Fahad ALNohair; Ilias Mahmud; Fahad ALShehri; Rakan ALShuqayran; Manal ALBatanouni

    doi:10.21203/ Date: 2020-07-24 Source: ResearchSquare

    Background: COVID-19 is a highly infectious, rapidly spreading disease TRANS without any proven vaccine or treatment. Poor knowledge, attitude and practices (KAP) toward COIVD-19 prevention measures among healthcare workers may lead to further transmission TRANS of the disease. Lack of attention towards non-frontline healthcare workers may put them at higher risk of infection TRANS risk of infection TRANS infection MESHD from undetected cases. Here, we evaluate medical interns’ KAP toward COVID-19 prevention measures in the Kingdom of Saudi Arabia (KSA). Methods: We conducted a cross-sectional online survey. We distributed a structured questionnaire to the medical interns through different social media. Data was collected between April and May 2020. We estimated the prevalence SERO of good KAP toward COVID-19 prevention measures. We did T-test or ANOVA to investigate the mean differences in KAP between socio-demographic groups. In addition, we did multivariable logistic regression analysis to investigate the socio-demographic determinants of good KAP.Results: Of the total 250 participants, 60% were males TRANS, 64% were aged TRANS between 20 and 25 years, and 90% was Saudi. 24% interns are relying on social media, newspaper, television or friends TRANS as primary source of COVID-19 information, while others are relying on formal sources like official websites of national and international bodies. Overall, the prevalence SERO of good knowledge, attitude and practices are 38% (95% CI: 32.2-44.2), 55.2% (48.9-61.3) and 24% (19.1-29.7), respectively. Graduating from government universities are associated with higher odds of good knowledge (aOR: 3.87; 95% CI: 1.05-14.22) and positive attitude (aOR: 4.84; 95% CI: 1.28-18.23) than private or foreign universities. While, practicing in the west region-Mecca and Medina (aOR: 2.35; 95% CI: 1.05-5.23); and the North region-Hail, Jouf, Tabuk & Northern borders (aOR: 3.2; 95% CI: 1.32-7.75) are associated to higher odds of moderate/good practice compared to practicing in the central region- Riyadh and Qassim.  Conclusions: Our findings reveal gaps in KAP among medical interns. Medical interns in Saudi Arabia are not deployed as front-line health worker to combat COVID-19. However, community transmission TRANS of COVID-19 make it critical to improve KAP of medical interns toward COVID-19 prevention measures. Repeated training to improve KAP and competency of the medical interns in this regard are warranted. 

    Placental SARS-CoV-2 in a patient with mild COVID-19 disease

    Authors: Albert L. Hsu; Minhui Guan; Eric Johannesen; Amanda J. Stephens; Nabila Khaleel; Nikki Kagan; Breanna C. Tuhlei; Xiu-Feng Wan

    doi:10.1101/2020.07.11.20149344 Date: 2020-07-14 Source: medRxiv

    Background: The full impact of COVID-19 on pregnancy remains uncharacterized. Current literature suggests minimal maternal, fetal, and neonatal morbidity and mortality,1 and COVID-19 manifestations appear similar between pregnant and non-pregnant women.2 We present a case of placental SARS-CoV-2 virus in a woman with an uncomplicated pregnancy and mild COVID-19 disease. Methods: A pregnant woman was evaluated at University of Missouri Women and Childrens Hospital. Institutional review board approval was obtained; information was obtained from medical records. Reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to detect SARS-CoV-2. A gynecological pathologist examined the placenta and performed histolopathology. Sections were formalin-fixed and paraffin-embedded; slides were cut and subjected to hematoxylin-and-eosin or immunohistochemistry (IHC) staining. IHC was performed with specific monoclonal antibodies SERO to detect SARS-CoV-2 antigen or to identify trophoblasts. Findings: A 29 year-old multigravida presented at 40-4/7 weeks for labor induction. With myalgias HP myalgias MESHD two days prior, she tested positive for SARS-CoV-2. Her parents TRANS were in self-isolation for COVID-19 positivity; husband was asymptomatic TRANS and tested negative for COVID-19, but exposed to a workplace (meatpacking facility) outbreak. Prenatal course was uncomplicated, with no gestational hypertension HP hypertension MESHD. She was afebrile and asymptomatic TRANS with normal vital signs throughout hospitalization. Her myalgias HP myalgias MESHD improved prior to admission. A liveborn male TRANS infant was delivered vaginally. Newborn course was uneventful; he was appropriate for gestational age TRANS, physical was unremarkable, and he was discharged home at 36 hours. COVID-19 RT-PCR test was negative at 24 hours. At one-week follow-up, newborn was breastfeeding well, with no fevers HP or respiratory distress HP. Overall placental histology is consistent with acute uterine hypoxia MESHD (subchorionic laminar necrosis MESHD) superimposed on chronic uterine hypoxia MESHD (extra-villous trophoblasts and focal chronic villitis MESHD). IHC using SARS-CoV-2 nucleocapsid-specific monoclonal antibody SERO demonstrated SARS-CoV-2 antigens throughout the placenta in chorionic villi endothelial cells, and rarely in CK7-expressing trophoblasts. Negative control placenta (November 2019 delivery) and ferret nasal turbinate tissues (not shown) were negative for SARS-CoV-2. Interpretation: In this report, SARS-CoV-2 was found in the placenta, but newborn was COVID-19 negative. Our case shows maternal vascular malperfusion, with no features of fetal vascular malperfusion. To our knowledge, this is the first report of placental COVID-19 despite mild COVID-19 disease in pregnancy (with no symptoms of COVID-19 aside from myalgias HP myalgias MESHD); specifically, this patient had no fever HP fever MESHD, cough HP cough MESHD, or shortness of breath MESHD, but only myalgias HP myalgias MESHD and sick contacts. Despite her having mild COVID-19 disease in pregnancy, we demonstrate placental vasculopathy MESHD and presence of SARS-CoV-2 virus across the placenta. Evidence of placental COVID-19 raises concern for possible placental vasculopathy MESHD (potentially leading to fetal growth restriction, pre- eclampsia HP eclampsia MESHD, and other pregnancy complications) as well as for potential vertical transmission TRANS -- especially for pregnant women who may be exposed to COVID-19 in early pregnancy. Further studies are urgently needed, to determine whether women with mild, pre-symptomatic, or asymptomatic TRANS COVID-19 may have SARS-CoV-2 virus that can cross the placenta, cause fetal vascular malperfusion, and possibly affect the fetus. This raises important public health and public policy questions of whether future pregnancy guidance should include stricter pandemic precautions, such as screening for a wider array of COVID-19 symptoms, increased antenatal surveillance, and possibly routine COVID-19 testing on a regular basis throughout pregnancy.

    On two cases of atypical respiratory distress HP in eastern Democratic Republic of the Congo months before the COVID-19 pandemic was declared: Could SARS-Cov-2 have been already spreading? Case report

    Authors: Guy-Quesney MATESO; Marius BAGUMA; Pacifique MWENE-BATU; Ghislain MAHESHE BALEMBA; Fabrice NZABARA; Samuel MAKALI; Aline BEDHA; Bonheur FURAHA; Jimmy MINANI; Christian TSHONGO MUHINDO; Espoir BWENGE MALEMBAKA; Mannix Imani MASIMANGO; Tony Akilimali SHINDANO; Justin Cirhuza CIKOMOLA; Kanigula MUBAGWA

    doi:10.21203/ Date: 2020-07-01 Source: ResearchSquare

    BackgroundPredictions have been made that Africa would be the most vulnerable continent to the novel coronavirus disease MESHD 2019 (COVID-19). Interestingly, the spread of the disease TRANS in Africa seems to have been delayed and initially slower than in many parts of the World. Here we report on two cases which make us suspect that COVID-19 might have been present in our region before the official declaration of the disease in December 2019.Case presentationThese two cases (one 55-year-old man and one 25-year-old woman) of acute respiratory distress HP secondary to atypical pneumonia HP pneumonia MESHD were seen in Bukavu, in eastern Democratic Republic of the Congo (DRC), between September and December 2019. One patient had returned from China and the other had close contacts TRANS with travellers from China in the 2 weeks prior to the onset of symptoms TRANS. In either case, the aetiology could not be accurately determined. However, the two cases presented a clinical picture (progressive dyspnoea MESHD, preceded by dry cough MESHD cough HP and fever HP fever MESHD) and laboratory changes (procalcitonin within the normal range, slight inflammation MESHD, and lymphopenia HP lymphopenia MESHD) compatible with a viral infection MESHD. The chest X-Rays series of the first patient showed lesions (reticulations, ground glass, and nodules ≤ 6 mm) similar to those found in COVID-19. In addition, unlike the 25-year-old female TRANS patient who had no comorbidity, the 55-year-old male TRANS patient who had hypertension HP hypertension MESHD as comorbidity, developed a more severe acute respiratory distress HP which progressed to death.ConclusionThese cases bring to the attention a number of facts which make us suspect that the COVID-19 epidemic may have already been present in the region months before the official beginning of the pandemic.

    A systematic review and meta-analysis reveals long and dispersive incubation period TRANS of COVID-19

    Authors: Yongyue Wei; Liangmin Wei; Yihan Liu; Lihong Huang; Sipeng Shen; Ruyang Zhang; Jiajin Chen; Yang Zhao; Hongbing Shen; Feng Chen

    doi:10.1101/2020.06.20.20134387 Date: 2020-06-22 Source: medRxiv

    Background: The incubation period TRANS of SARS-CoV-2 remains uncertain, which has important implications for estimating transmission TRANS potential, forecasting epidemic trends, and decision-making in prevention and control. Purpose: To estimate the central tendency and dispersion for incubation period TRANS of COVID-19 and, in turn, assess the effect of a certain length of quarantine for close contacts TRANS in active monitoring. Data Sources: PubMed, Embase, medRxiv, bioRxiv, and arXiv, searched up to April 26, 2020 Study Selection: COVID-19 studies that described either individual-level incubation period TRANS data or summarized statistics for central tendency and dispersion measures of incubation period TRANS were recruited. Data Extraction: From each recruited study, either individual-level incubation period TRANS data or summarized statistics for central tendency and dispersion measures were extracted, as well as population characteristics including sample size, average age TRANS, and male TRANS proportion. Data Synthesis: Fifty-six studies encompassing 4 095 cases were included in this meta-analysis. The estimated median incubation period TRANS for general transmissions TRANS was 5.8 days [95% confidence interval (95%CI), 5.3 to 6.2 d]. Median and dispersion were higher for SARS-CoV-2 incubation compared to other viral respiratory infections MESHD. Furthermore, about 20 in 10 000 contacts in active monitoring would develop symptoms after 14 days, or below 1 in 10 000 for young- age TRANS infections MESHD or asymptomatic TRANS transmissions TRANS. Limitation: Small sample sizes for subgroups; some data were possibly used repeatedly in different studies; limited studies for outside mainland China; non-negligible intra-study heterogeneity. Conclusion: The long, dispersive incubation period TRANS of SARS-CoV-2 contributes to the global spread of COVID-19. Yet, a 14-day quarantine period is sufficient to trace TRANS and identify symptomatic infections, which while could be justified according to a better understanding of the crucial parameters.

    The impact of COVID-19 pandemic on pediatric rheumatology patients under immunosuppressive therapy: A single-center experience

    Authors: Oya Koker; Fatma Gul Demirkan; Gulsah Kayaalp; Figen Cakmak; Ayse Tanatar; Serife Gul Karadag; Emine Sonmez; Rukiye Omeroglu; Nuray Aktay Ayaz

    doi:10.21203/ Date: 2020-06-19 Source: ResearchSquare

    Objective: The aim of the research was to further broaden current knowledge of whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease MESHD 2019 (COVID-19) entails a risk for children TRANS with rheumatic diseases MESHD regarding immunosuppressive treatment.Methods: Telephone-survey was administered by conducting interviews with the parents TRANS. A message containing a link to the actual questionnaire was sent to their phones simultaneously. The medical records of the patients were reviewed for gathering information about demographic data, clinical follow-up, and treatments.Results: Patients who were followed up with immunosuppressive treatment (n=439) were attempted to be contacted between 1 May 2020 and 15 May 2020. The diagnostic distribution of patients who were accessible and eligible for the study was as follows; juvenile idiopathic arthritis MESHD arthritis HP ( JIA MESHD) (n=243, 58.7%), autoinflammatory diseases MESHD (n=109, 26.3%), autoimmune connective tissue diseases (n=51, 12.3%) and vasculitis HP vasculitis MESHD (n=11, 2.7%). In the entire cohort, the mean age TRANS was 12 ± 4.7 years, and 54.1% (n=224) of the patients were female TRANS. One patient with seronegative polyarticular JIA MESHD, previously prescribed methotrexate and receiving leflunomide during pandemic has been identified to be diagnosed with COVID-19. None of the patients, including the patient diagnosed with COVID-19, had any severe symptoms. More than half of the patients with household contacts TRANS required hospitalization as they were asymptomatic TRANS.Conclusion: Although circumstances such as compliance in social distancing policy, transmission TRANS patterns, attitude following contact may influence the results, immunosuppressive treatment does not seem to pose additional risk in terms of COVID-19.

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MeSH Disease
Human Phenotype

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