### Overview

MeSH Disease

Infections (545)

Disease (225)

Death (190)

Human Phenotype

Fever (61)

Pneumonia (56)

Cough (48)

Fatigue (12)

Hypertension (11)

Transmission

Seroprevalence
displaying 1 - 10 records in total 560
records per page

### Genomic epidemiology reveals transmission TRANS patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Authors: Jemma L Geoghegan; Xiaoyun Ren; Matthew Storey; James Hadfield; Lauren Jelley; Sarah Jefferies; Jill Sherwood; Shevaun Paine; Sue Huang; Jordan Douglas; Fabio K L Mendes; Andrew Sporle; Michael G Baker; David R Murdoch; Nigel French; Colin R Simpson; David Welch; Alexei J Drummond; Edward C Holmes; Sebastian Duchene; Joep de Ligt

doi:10.1101/2020.08.05.20168930 Date: 2020-08-06 Source: medRxiv

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand has now effectively eliminated the virus, with low numbers of new cases limited to new arrivals in managed quarantine facilities at the border. Here, we generated 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected between 26 February and 22 May 2020, representing 56% of all confirmed cases TRANS in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number TRANS, Re, of New Zealand's largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission TRANS lineage of more than one additional case. Most of the cases that resulted in a transmission TRANS lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections MESHD to a major transmission TRANS cluster than through epidemiological data alone, providing probable sources of infections MESHD for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease MESHD mitigation.

### Analysis of COVID-19 and comorbidity co- infection MESHD Model with Optimal Control

Authors: Dr. Andrew Omame; Nometa Ikenna

doi:10.1101/2020.08.04.20168013 Date: 2020-08-04 Source: medRxiv

The new coronavirus disease MESHD 2019 (COVID-19) infection MESHD is a double challenge for people infected with comorbidities such as cardiovascular and cerebrovascular diseases MESHD and diabetes. Comorbidities have been reported to be risk factors for the complications of COVID-19. In this work, we develop and analyze a mathematical model for the dynamics of COVID-19 infection MESHD in order to assess the impacts of prior comorbidity on COVID-19 complications and COVID-19 re- infection MESHD. The model is simulated using data relevant to the dynamics of the diseases MESHD in Lagos, Nigeria, making predictions for the attainment of peak periods in the presence or absence of comorbidity. The model is shown to undergo the phenomenon of backward bifurcation caused by the parameter accounting for increased susceptibility to COVID-19 infection MESHD by comorbid susceptibles as well as the rate of re- infection MESHD by those who have recovered from a previous COVID-19 infection MESHD. Sensitivity SERO analysis of the model when the population of individuals co-infected with COVID-19 and comorbidity is used as response function revealed that the top ranked parameters that drive the dynamics of the co- infection MESHD model are the effective contact rate for COVID-19 transmission TRANS, $\beta\sst{cv}$, the parameter accounting for increased susceptibility to COVID-19 by comorbid susceptibles, $\chi\sst{cm}$, the comorbidity development rate, $\theta\sst{cm}$, the detection rate for singly infected and co-infected individuals, $\eta_1$ and $\eta_2$, as well as the recovery rate from COVID-19 for co-infected individuals, $\varphi\sst{i2}$. Simulations of the model reveal that the cumulative confirmed cases TRANS (without comorbidity) may get up to 180,000 after 200 days, if the hyper susceptibility rate of comorbid susceptibles is as high as 1.2 per day. Also, the cumulative confirmed cases TRANS (including those co-infected with comorbidity) may be as high as 1000,000 cases by the end of November, 2020 if the re- infection MESHD rates for COVID-19 is 0.1 per day. It may be worse than this if the re- infection MESHD rates increase higher. Moreover, if policies are strictly put in place to step down the probability of COVID-19 infection MESHD by comorbid susceptibles to as low as 0.4 per day and step up the detection rate for singly infected individuals to 0.7 per day, then the reproduction number TRANS can be brought very low below one, and COVID-19 infection MESHD eliminated from the population. In addition, optimal control and cost-effectiveness analysis of the model reveal that the the strategy that prevents COVID-19 infection MESHD by comorbid susceptibles has the least ICER and is the most cost-effective of all the control strategies for the prevention of COVID-19.

### Characteristics of COVID-19 fatality cases in East Kalimantan, Indonesia

Authors: Swandari Paramita; Ronny Isnuwardana; Krispinus Duma; Rahmat Bakhtiar; Muhammad Khairul Nuryanto; Riries Choiru Pramulia Yudia; Evi Fitriany; Meiliati Aminyoto

doi:10.1101/2020.08.01.20166470 Date: 2020-08-04 Source: medRxiv

Introduction. Coronavirus Disease MESHD (COVID-19) is caused by SARS-CoV-2 infection MESHD. On March 2, 2020, Indonesia announced the first confirmed cases TRANS of COVID-19 infection MESHD. East Kalimantan will play an important role as the new capital of Indonesia. There is attention to the preparedness of East Kalimantan to respond to COVID-19. We report the characteristics of COVID-19 fatality cases in here. Methods. We retrospectively analyzed the fatality cases of COVID-19 patients from the East Kalimantan Health Office information system. All patients were confirmed COVID-19 by RT-PCR examination. Results. By July 31, 2020, 31 fatality cases of patients had been identified as having confirmed COVID-19 in East Kalimantan. The mean age TRANS of the patients was 55.1 + 9.2 years. Most of the patients were men (22 [71.0%]) with age TRANS more than 60 years old (14 [45.2%]). Balikpapan has the highest number of COVID-19 fatality cases from all regencies. Hypertension MESHD Hypertension HP was the most comorbidities in the fatality cases of COVID-19 patients in East Kalimantan. Discussion. Older age TRANS and comorbidities still contributed to the fatality cases of COVID-19 patients in East Kalimantan, Indonesia. Hypertension MESHD Hypertension HP, diabetes, cardiovascular disease MESHD, and cerebrovascular disease MESHD were underlying conditions for increasing the risk of COVID-19 getting into a serious condition. Conclusion. Active surveillance for people older than 60 years old and having underlying diseases MESHD is needed for reducing the case fatality rate of COVID-19 in East Kalimantan. Keywords. Comorbidity, fatality cases, COVID-19, Indonesia.

### Clinical course and severity outcome indicators among COVID 19 hospitalized patients in relation to comorbidities distribution Mexican cohort

Authors: Genny Carrillo; Nina Mendez Dominguez; Kassandra D Santos Zaldivar; Andrea Rochel Perez; Mario Azuela Morales; Osman Cuevas Koh; Alberto Alvarez Baeza

doi:10.1101/2020.07.31.20165480 Date: 2020-08-04 Source: medRxiv

Introduction: COVID-19 affected worldwide, causing to date, around 500,000 deaths MESHD. In Mexico, by April 29, the general case fatality was 6.52%, with 11.1% confirmed case TRANS mortality and hospital recovery rate around 72%. Once hospitalized, the odds for recovery and hospital death MESHD rates depend mainly on the patients' comorbidities and age TRANS. In Mexico, triage guidelines use algorithms and risk estimation tools for severity assessment and decision-making. The study's objective is to analyze the underlying conditions of patients hospitalized for COVID-19 in Mexico concerning four severity outcomes. Materials and Methods: Retrospective cohort based on registries of all laboratory-confirmed patients with the COVID-19 infection MESHD that required hospitalization in Mexico. Independent variables were comorbidities and clinical manifestations. Dependent variables were four possible severity outcomes: (a) pneumonia MESHD pneumonia HP, (b) mechanical ventilation (c) intensive care unit, and (d) death MESHD; all of them were coded as binary Results: We included 69,334 hospitalizations of laboratory-confirmed and hospitalized patients to June 30, 2020. Patients were 55.29 years, and 62.61% were male TRANS. Hospital mortality among patients aged TRANS<15 was 9.11%, 51.99% of those aged TRANS >65 died. Male TRANS gender TRANS and increasing age TRANS predicted every severity outcome. Diabetes and hypertension MESHD hypertension HP predicted every severity outcome significantly. Obesity MESHD Obesity HP did not predict mortality, but CKD, respiratory diseases MESHD, cardiopathies were significant predictors. Conclusion: Obesity MESHD Obesity HP increased the risk for pneumonia MESHD pneumonia HP, mechanical ventilation, and intensive care admittance, but it was not a predictor of in-hospital death MESHD. Patients with respiratory diseases MESHD were less prone to develop pneumonia MESHD pneumonia HP, to receive mechanical ventilation and intensive care unit assistance, but they were at higher risk of in-hospital death MESHD.

### Risk stratification as a tool to rationalize quarantine among health care workers exposed to COVID-19 cases - Evidence from a tertiary healthcare centre in India

Authors: Ravneet Kaur; Shashi Kant; Mohan Bairwa; Arvind Kumar; Shivram Dhakad; Vignesh Dwarakanathan; Aftab Ahmad; Pooja Pandey; Arti Kapil; Rakesh Lodha; Naveet Wig

doi:10.1101/2020.07.31.20166264 Date: 2020-08-04 Source: medRxiv

Background: Quarantine of healthcare workers (HCWs) exposed to COVID 19 confirmed cases TRANS is a well known strategy for limiting the transmission TRANS of infection MESHD. However, there is a need for evidence-based guidelines for the quarantine of HCWs in COVID 19. Methods: We describe our experience of contact tracing TRANS and risk stratification of 3853 HCWs who were exposed to confirmed COVID-19 cases in a tertiary health care institution in India. We developed an algorithm, on the basis of risk stratification, to rationalize quarantine among HCWs. Risk stratification was based on the duration of exposure, distance from the patient, and appropriateness of personal protection equipment (PPE) usage. Only high-risk contacts were quarantined for 14 days. They underwent testing for COVID 19 after five days of exposure, while low risk contacts continued their work with adherence to physical distancing, hand hygiene, and appropriate use of PPE. The low-risk contacts were encouraged to monitor for symptoms and report for COVID 19 screening if fever MESHD fever HP, cough MESHD cough HP, or shortness of breath occurred. We followed up all contacts for 14 days from the last exposure and observed for symptoms of COVID 19 and test positivity. Results and interpretation: Out of total 3853 contacts, 560 (14.5%) were categorized as high-risk contacts, and 40 of them were detected positive for COVID 19, with a test positivity rate of 7.1% (95% CI = 5.2, 9.6). Overall, 118 (3.1%) of all contacts tested positive. Our strategy prevented 3215 HCWs from being quarantined and saved 45,010 person-days of health workforce until June 8, 2020, in the institution. We conclude that exposure-based risk stratification and quarantine of HCWs is a viable strategy to prevent unnecessary quarantine, in a healthcare institution.

### Study on the COVID-19 infection MESHD status, prevention and control strategies among entry people in Shenzhen

Authors: Jing-Zhong Wang; Xuan Zou; Zi-Qian Xu; Hai-Rui Wang; Bi-Xin Wang; Jian-Fan He

doi:10.21203/rs.3.rs-52913/v1 Date: 2020-08-03 Source: ResearchSquare

Background The COVID-19 confirmed cases TRANS overseas continue to rise for months, while people overseas prefer to return at present. It is risky to have a large number of infected imported cases which may cause COVID-19 spread to China and even lead to outbreak again. In order to prevent imported infection MESHD, Shenzhen implemented the losed-loop management strategy by taking nucleic acid testing (NAT) for severe acute respiratory syndromes MESHD coronavirus 2 (SARS-CoV-2) and medical observation for 14 days among individuals who have epidemic history (Hong Kong, Macao, Taiwan province and other countries) within 14 days. Our study described the status of COVID-19 infection MESHD among entry people in Shenzhen, and also evaluated the effect of closed-loop management strategy.Methods A total of 86,844 people overseas entered Shenzhen from January 1 to April 18, 2020, and there were 39 imported cases. We made a descriptive study by analyzing the entry time, reported time, local confirmed cases TRANS in origin countries, and the number of entry people from abroad. The NAT were completed in Shenzhen center for disease MESHD control and prevention (CDC), ten district-level CDCs, as well as fever MESHD fever HP clinics.Results The infection MESHD rate of entry people was 4.49‰ (95% CI: 3.26‰ − 6.05‰). Most of the entry people or imported cases have Chinese nationality. The number of entry people and imported cases in Nanshan and Futian districts were larger than others. 15.73% of the entry people came from the US, and 12.67% came from the UK. 14 imported cases (35.9%) came from the UK, 9 (23.08%) came from the US. The imported risks from the US and UK in Shenzhen were higher than other countries or regions. According to the 14-days’ incubation period TRANS and the number of entry people, individuals from the US since Mar 9 were the high-risk population. Accordingly, entry people from the UK since Mar 13 were the high-risk population. It is important to evaluate the imported risk by analyzing local confirmed cases TRANS status in origin countries or regions and the number of entry people from these countries or regions to Shenzhen. The distribution of entry time and report time for imported cases in Shenzhen were similar. So it is important to prevent and control COVID-19 imported infection MESHD by taking NAT and medical observation at port.Conclusions It is effective to implement closed-loop management strategy for individuals who have epidemic history (Hong Kong, Macao, Taiwan province and other countries) within 14 days. In order to control COVID-19 outbreak, we need the collaboration and cooperation at the global, national, and subnational levels to prevent, detect, and respond effectively.

### Infected hip prosthesis in patient with suspected Covid-19 infection MESHD

Authors: Dr. Andrea Cosentino; Dr. Gianni Odorizzi; Dr. Wilhelm Berger

doi:10.21203/rs.3.rs-53032/v1 Date: 2020-08-03 Source: ResearchSquare

Background: Infections MESHD following arthroplasty are one of the major risks during this type of surgery.Case presentation: Four and half years after right hip arthroplasty surgery, the patient came back to our attention with pain MESHD pain HP at the same hip. The instrumental examinations showed signs of cup detachment and therefore, after carefully analyzing the case, we decided to perform a sterile aspiration HP of the hip in the operating room under C-arm fluoroscopy. Microbiological examinations showed positivity for E.Coli. The patient underwent to surgery to remove the prosthesis and implant a spacer. A therapy with Cefotaxim 2g 1-1-1 for 6 weeks was then set, after which a total arthroplasty was implanted. During this period, the Covid-19 pandemic occurred and therefore the patient performed two nasal-throat swabs, both negative. However, one week after the final surgery, respiratory conditions worsened and we performed a chest X-ray and CT scan, with suggestive images of ground-glass opacification patterns (GGO). Due to the clinic and the characteristic images of the instrumental examinations, the patient was transferred to the observation ward, waiting for the response of two additional swabs, also negative. The patient was then transferred to the ward for patients with typical symptoms of Covid-19 but with negative swabs for two weeks and subsequently discharged at home.Conclusion: Despite the concomitant Covid-19 pandemic, the guidelines in case of periprosthetic hip infection MESHD infection further confirm TRANS further confirm the correct management of the patient.

### Modeling latent infection MESHD transmissions TRANS through biosocial stochastic dynamics

doi:10.1101/2020.07.30.20164491 Date: 2020-08-01 Source: medRxiv

The events of the recent SARS-CoV-02 epidemics have shown the importance of social factors, especially given the large number of asymptomatic TRANS cases that effectively spread the virus, which can cause a medical emergency MESHD to very susceptible individuals. Besides, the SARS-CoV-02 virus survives for several hours on different surfaces, where a new host can contract it with a delay. These passive modes of infection MESHD transmission TRANS remain an unexplored area for traditional mean-field epidemic models. Here, we design an agent-based model for simulations of infection MESHD transmission TRANS in an open system driven by the dynamics of social activity; the model takes into account the personal characteristics of individuals, as well as the survival time of the virus and its potential mutations. A growing bipartite graph embodies this biosocial process, consisting of active carriers TRANS (host) nodes that produce viral nodes during their infectious period TRANS. With its directed edges passing through viral nodes between two successive hosts, this graph contains complete information about the routes leading to each infected individual. We determine temporal fluctuations of the number of exposed and the number of infected individuals, the number of active carriers TRANS and active viruses at hourly resolution. The simulated processes underpin the latent infection MESHD transmissions TRANS, contributing significantly to the spread of the virus within a large time window. More precisely, being brought by social dynamics and exposed to the currently existing infection MESHD, an individual passes through the infectious state until eventually spontaneously recovers or otherwise is moves to a controlled hospital environment. Our results reveal complex feedback mechanisms that shape the dependence of the infection MESHD curve on the intensity of social dynamics and other sociobiological factors. In particular, the results show how the lockdown effectively reduces the spread of infection MESHD and how it increases again after the lockdown is removed. Furthermore, a reduced level of social activity but prolonged exposure of susceptible individuals have adverse effects. On the other hand, virus mutations that can gradually reduce the transmission TRANS rate by hopping to each new host along the infection MESHD path can significantly reduce the extent of the infection MESHD, but can not stop the spreading without additional social strategies. Our stochastic processes, based on graphs at the interface of biology and social dynamics, provide a new mathematical framework for simulations of various epidemic control strategies with high temporal resolution and virus traceability.

### 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.

### Long-term patient-reported symptoms of COVID-19: an analysis of social media data

Authors: Juan M. Banda; Gurdas Viguruji Singh; Osaid Alser; DANIEL PRIETO-ALHAMBRA

doi:10.1101/2020.07.29.20164418 Date: 2020-08-01 Source: medRxiv

As the COVID-19 virus continues to infect people across the globe, there is little understanding of the long term implications for recovered patients. There have been reports of persistent symptoms after confirmed infections TRANS infections MESHD on patients even after three months of initial recovery. While some of these patients have documented follow-ups on clinical records, or participate in longitudinal surveys, these datasets are usually not publicly available or standardized to perform longitudinal analyses on them. Therefore, there is a need to use additional data sources for continued follow-up and identification of latent symptoms that might be underreported in other places. In this work we present a preliminary characterization of post-COVID-19 symptoms using social media data from Twitter. We use a combination of natural language processing and clinician reviews to identify long term self-reported symptoms on a set of Twitter users.

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 All None MeSH Disease Human Phenotype Transmission Seroprevalence

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