### Overview

MeSH Disease

Human Phenotype

Fever (3)

Pneumonia (3)

Dyspnea (2)

Falls (1)

Cough (1)

Transmission

Transmission (16)

fomite (3)

Seroprevalence
displaying 1 - 10 records in total 16
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### Unexpected Co-infection MESHD with Different Strains of SARS-CoV-2 in Patients with COVID-19

Authors: Hayder O. Hashim; Mudher K. Mohammed; Mazin J. Mousa; Hadeer H. Abdulameer; Alaa T.S. Alhassnawi; Safa A. Hassan; Mohammed Baqur S. Al-Shuhaib

id:10.20944/preprints202009.0375.v1 Date: 2020-09-17 Source: Preprints.org

There is a rising global concern for the ongoing outbreak of SARS-CoV-2 due to its high transmission TRANS rate and unavailability of treatment. Through the binding of its spike glycoprotein with angiotensin type 2 (ACE2), SARS-CoV-2 can efficiently get in the cells of patients and start its pandemic cycle. Herein, the biological diversity of SARS-CoV-2 infection MESHD was assessed in Babylon province of Iraq by investigating the possible genetic variations of the spike glycoprotein. A specific coding region of 795 bp within the viral spike (S) gene was amplified from 19 patients who suffered from obvious symptoms of SARS-CoV-2 infection MESHD. Sequencing results identified fifteen novel nucleic acid variations with a variety of distributions within the investigated samples. The electropherograms of all the identified variations showed obvious co-infections MESHD with at least two different viral strains per sample. Within these co-infections, the majority of samples exhibited three nonsense single nucleotide polymorphism (SNP)s, p.301Cdel, p.380Ydel, and p.436del, which yielded three truncated SARS-CoV-2 spike glycoproteins of 301, 380, and 436 amino acids length, respectively. The network and phylogenetic analyses indicated that for all viral infections were derived from multi-ancestral origins. Results inferred from the specific clade-based tree entailed that some viral strains were derived from European G-clade sequences. In conclusion, our data demonstrated the absence of any single strain infection MESHD among all investigated viral samples in the studied area, which may entail a higher risk of SARS-CoV-2 in this country. Through the identified high frequency of truncated spike proteins, we suggest that defective SARS-CoV-2 may depend on helper strains having intact spikes in its infection. Alternatively, another putative ACE2-independent route of viral infection MESHD way also suggested. To the best of our knowledge, this is the first report to describe the co-infection MESHD of multiple strains of SARS-CoV-2 in patients with COVID-19.

### Does Respiratory Co-Infection MESHD Facilitate Dispersal of SARS-CoV-2? Investigation of a Super-Spreading Event in an Open-Space Office

Authors: Dana Weissberg; Jürg Böni; Silvana Rampini; Verena Kufner; Maryam Zaheri; Peter W. Schreiber; Irene A. Abela; Michael Huber; Hugo Sax; Aline Wolfensberger

doi:10.21203/rs.3.rs-73054/v1 Date: 2020-09-06 Source: ResearchSquare

Background: Super-spreaders are individuals infecting disproportionately large numbers of contacts. They probably play a crucial role in the transmission TRANS of severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). We describe a super-spreading event within a team working in an open-space office and investigate factors potentially having facilitated SARS-CoV-2 transmission TRANS.Methods: In this retrospective cohort study, semi-structured telephone interviews with all team members were carried out to identify symptoms, contacts, and adherence to basic hygiene measures. During site visits, we gathered information about workplace and seating arrangements. The secondary attack rate TRANS in office and households was calculated. Potential respiratory viral co-infections MESHD were assessed by multiplex PCR. SARS-CoV-2 whole-genome sequencing was performed using a tiled-amplicon sequencing approach.Results: Of 13 team members, 11 fell HP ill with Coronavirus disease MESHD 2019 (COVID-19). Due to the sequence of events and full genome sequence data, one person was considered the index case for this outbreak, directly infecting 67% to 83% of the teammates. All team members reported repetitive close contacts TRANS among themselves during joint computer work, team meetings and a “Happy Birthday” serenade. Two individuals shared nuts and dates. The arrangement of the office and meeting rooms precluded sufficient adherence to physical distancing. The index case and a further individual were diagnosed with an adenovirus serotype 4 co-infection MESHD, but secondary household attack rate TRANS was not higher for co-infected MESHD individuals. Conclusion: We identified several environmental and behavioral factors that probably have facilitated the transmission TRANS of SARS-CoV-2. The relevance of the adenovirus co-infection MESHD remains unclear and merits further investigation.

### Kawasaki Disease MESHD Outbreak in Children TRANS During COVID-19 Pandemic.

Authors: Ewelina Gowin; Jacek Wysocki; Magdalena Frydrychowicz; Danuta Januszkiewicz-Lewandowska

doi:10.21203/rs.3.rs-70123/v1 Date: 2020-09-01 Source: ResearchSquare

### How Efficient is Contact Tracing TRANS in Mitigating the Spread of Covid-19? A Mathematical Modeling Approach

Authors: T. A. Biala; Y. O. Afolabi; A. Q. M. Khaliq

id:2008.03859v1 Date: 2020-08-10 Source: arXiv

Contact Tracing TRANS (CT) is one of the measures taken by government and health officials to mitigate the spread of the novel coronavirus. In this paper, we investigate its efficacy by developing a compartmental model for assessing its impact on mitigating the spread of the virus. We describe the impact on the reproduction number TRANS $\mathcal{R}_c$ of Covid-19. In particular, we discuss the importance and relevance of parameters of the model such as the number of reported cases, effectiveness of tracking and monitoring policy, and the transmission TRANS rates to contact tracing TRANS. We describe the terms perfect tracking'', perfect monitoring'' and perfect reporting'' to indicate that traced contacts TRANS will be tracked while incubating, tracked contacts are efficiently monitored so that they do not cause secondary infections MESHD, and all infected persons are reported, respectively. We consider three special scenarios: (1) perfect monitoring and perfect tracking of contacts of a reported case, (2) perfect reporting of cases and perfect monitoring of tracked reported cases and (3) perfect reporting and perfect tracking of contacts of reported cases. Furthermore, we gave a lower bound on the proportion of contacts to be traced TRANS to ensure that the effective reproduction, $\mathcal{R}_c$, is below one and describe $\mathcal{R}_c$ in terms of observable quantities such as the proportion of reported and traced TRANS cases. Model simulations using the Covid-19 data obtained from John Hopkins University for some selected states in the US suggest that even late intervention of CT may reasonably reduce the transmission TRANS of Covid-19 and reduce peak hospitalizations and deaths. In particular, our findings suggest that effective monitoring policy of tracked cases and tracking of traced contacts TRANS while incubating are more crucial than tracing TRANS more contacts.

### 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 MESHD with comorbidities such as cardiovascular and cerebrovascular diseases MESHD and diabetes MESHD. 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. The model is simulated using data relevant to the dynamics of the diseases 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 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 MESHD 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 MESHD individuals, $\eta_1$ and $\eta_2$, as well as the recovery rate from COVID-19 for co-infected MESHD 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 MESHD with comorbidity) may be as high as 1000,000 cases by the end of November, 2020 if the re-infection rates for COVID-19 is 0.1 per day. It may be worse than this if the re-infection 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 MESHD individuals to 0.7 per day, then the reproduction number TRANS can be brought very low below one, and COVID-19 infection 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.

### State-level tracking of COVID-19 in the United States

Authors: H Juliette T Unwin; Swapnil Mishra; Valerie C Bradley; Axel Gandy; Thomas A Mellan; Helen Coupland; Jonathan Ish-Horowicz; Michaela Andrea Christine Vollmer; Charles Whittaker; Sarah L Filippi; Xiaoyue Xi; Mélodie Monod; Oliver Ratmann; Michael Hutchinson; Fabian Valka; Harrison Zhu; Iwona Hawryluk; Philip Milton; Kylie E C Ainslie; Marc Baguelin; Adhiratha Boonyasiri; Nick F Brazeau; Lorenzo Cattarino; Zulma M Cucunubá; Gina Cuomo-Dannenburg; Ilaria Dorigatti; Oliver D Eales; Jeffrey W Eaton; Sabinee L van Elsland; Richard G FitzJohn; Katy A M Gaythorpe; William Green; Wes Hinsley; Benjamin Jeffrey; Edward Knock; Daniel J Laydon; John Lees; Gemma Nedjati-Gilani; Pierre Nouvellet; Lucy C Okell; Kris V Parag; Igor Siveroni; Hayley A Thompson; Patrick Walker; Caroline E Walters; Oliver J Watson; Lilith K Whittles; Azra Ghani; Neil M Ferguson; Steven Riley; Christl A. Donnelly; Samir Bhatt; Seth Flaxman

doi:10.1101/2020.07.13.20152355 Date: 2020-07-14 Source: medRxiv

As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths MESHD reported in the next most severely impacted country. We jointly modelled the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number TRANS (the average number of secondary infections TRANS secondary infections MESHD caused by an infected person). We used changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission TRANS of SARS-CoV-2. Nationally, we estimated 3.7% [3.4%-4.0%] of the population had been infected by 1st June 2020, with wide variation between states, and approximately 0.01% of the population was infectious. We also demonstrated that good model forecasts of deaths for the next 3 weeks with low error MESHD and good coverage of our credible intervals.

### Profiling pre-symptomatic and asymptomatic TRANS cases with confirmed TRANS SARS-CoV-2 infection MESHD in Mexico City

Authors: Omar Yaxmehen Bello-Chavolla; Neftali Eduardo Antonio-Villa; Arsenio Vargas-Vázquez; Carlos A. Fermín-Martínez; Alejandro Márquez-Salinas; Jessica Paola Bahena-López

doi:10.1101/2020.07.02.20145516 Date: 2020-07-04 Source: medRxiv

BACKGROUND: Asymptomatic TRANS SARS-CoV-2 infections MESHD are potential sources for transmission TRANS. OBJECTIVES: Here, we aimed to profile pre-symptomatic/ asymptomatic TRANS SARS-CoV-2 infections MESHD in Mexico City, its associated comorbidities and outcomes. METHODS: Prospective observational study of SARS-CoV-2 cases assessed by contact tracing TRANS within the National Epidemiological Surveillance System in Mexico City. We classified subjects as cases with and without respiratory and non-respiratory symptoms ( RS MESHD, NRS, respectively) assessed for SARS-CoV-2 using real time RT-PCR from nasopharyngeal swabs to evaluate clinical characteristics as well as features associated with severe COVID-19. RESULTS: Amongst 80735 cases with confirmed TRANS SARS-CoV-2 infection MESHD as of July 23th, 2020, we identified 9659 cases without RS MESHD (12.0%), 5605 had only NRS (6.9%) and 4054 who were initially asymptomatic TRANS (5.1%). Compared to asymptomatic TRANS cases, those with NRS and those with RS MESHD+NRS had higher rates of severe COVID-19 outcomes including hospitalization, ICU admission, and intubation (p<0.001). Mortality was higher for cases with RS MESHD+NRS (HR 7.58, 95%CI 4.56-12.58) or NRS (HR 3.13, 95%CI 1.80-5.45) compared to asymptomatic TRANS cases, adjusted for age TRANS, sex and comorbidities. Predictors for mortality in asymptomatic TRANS SARS-Co-V-2 infections MESHD infections, chronic HP chronic kidney disease MESHD, previous exposure with suspected infection MESHD cases and older age TRANS were predictors for lethality. CONCLUSIONS: Definition of pre-symptomatic/ asymptomatic TRANS cases has relevant implications for SARS-CoV-2 infection MESHD outcomes. Older age TRANS and comorbidity impact on the probability of developing severe complications for cases who were asymptomatic TRANS or had only NRS at evaluation and were sent for domiciliary treatment. Extending testing for detection of asymptomatic TRANS cases must be considered in Mexico to better understand the impact of the pandemic.

### Factors Affecting SARS-CoV-2 (COVID-19) Pandemic, including Zoonotic, Human Transmission and Chain TRANS of Infection. Reducing Public Health Risk by Serum SERO Antibody Testing SERO, Avoiding Screening in Unhygienic Places and False PCR Reporting. A Scientific Review

Authors: Kamran Mahmood Ahmed Aziz; Abdullah Othman; Waleed Alqahtani; Sumaiya Azhar

id:10.20944/preprints202006.0284.v1 Date: 2020-06-23 Source: Preprints.org

Since December 2019, a rapid increase in the number of SARS-CoV-2 (COVID-19) cases was reported worldwide, despite strict infection control and lock down measures. Current paper investigated the actual facts behind this rapid increase in the number of cases. Study of genomic sequence reveals that domestic and wild animals were likely ancestors and zoonotic source for SARS-CoVs MESHD, MERS-CoVs, and SARS-CoV-2. Strong evidence suggest that these viruses already existed and replicated in animals and humans during past several decades, exhibiting diverse mutations, evolutions and self-limiting diseases, except during outbreaks. Serious zoonotic reservoir investigations are required to investigate animal transmission TRANS of SARS-CoVs and SARS-CoV-2 MESHD to limit current pandemic. This might be the reason of increasing number of cases via animals. SARS-CoV-2 has been retrospectively isolated in different studies in August 2019, several months before Wuhan announced. Hence, there is a possibility that viruses existed, went undetected, infecting subclinically, in past several years, and SARS-CoV-2 antigens and neutralizing antibodies SERO may have been present in humans since long time. This might be another reason of increasing number of cases by screening as mass screening and antigen or antibody testing SERO was not carried out in the past years. Randomized controlled trials are required to investigate human to human transmission TRANS by touch, as the current evidence is limited with conflicting results. As all SARS-CoVs MESHD are basically respiratory viruses, droplet precautions and infection MESHD control measures are essential, especially for hospital staff. Increased number of SARS-CoV-2 asymptomatic TRANS, or subclinical cases are detected worldwide. This silent phase of transmission TRANS can be beneficial for humans. Lack of symptoms eventually lessen virus transmission TRANS and reduce the pathogen's long-term survival and provide humoral herd immunity up to several years. Hence, seropositivity with diverse antibodies SERO develops against mutating SARS-CoVs which will confer strong immunity during epidemics. Strategies such as identification, contact tracing TRANS and quarantine are costly and practically difficult. Hence, asymptomatic TRANS persons can continue their work with droplet precautions and standard infection control procedures, while symptomatic or sick persons can isolate themselves in their homes without the need for strict quarantine until clinical recovery, with reduced hospital visits and minimizing chances of hospital acquired infections. RT-PCR has low sensitivity SERO and specificity, carries a high risk of handling live virus antigens, and requires difficult protocols. As viral load also sharply declines after few days of onset of infection MESHD, this technique might overlook infection MESHD. Furthermore, SARS-CoV-2 infection MESHD may be present in blood SERO when oropharyngeal swabs are negative by RT-PCR. Additionally, RT-PCR usually gives false negative and false positive results and must be interpreted cautiously. This might be again a reason of increasing number of cases by false positive RT-PCR reporting. Moreover, antibodies SERO against SARS-CoVs develop robustly in serum SERO even by reduced amount of antigens. In contrast to RT-PCR, ELISA SERO for diagnosing antibodies SERO against SARS-CoV-2 demonstrates 100% specificity and 100% sensitivity SERO, even in clinically asymptomatic TRANS individuals. These antibodies SERO can be used for serologic surveys SERO, monitoring and screening. However, screening tests for SARS-COV-2 should be avoided in unhygienic public places by nasopharyngeal swabs, which carry a high risk of further transmission TRANS, co-infection MESHD or superinfection. Such highly infectious virus must be isolated and tested in highly sterilized laboratory. Further strict international laws and policies are required to stop the possible spread of experimental viruses, biological warfare and bioterrorism.

### Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans

Authors: Oscar A MacLean; Spyros Lytras; Steven Weaver; Joshua B Singer; Maciej F Boni; Philippe Lemey; Sergei L Kosakovsky Pond; David L Robertson

doi:10.1101/2020.05.28.122366 Date: 2020-05-29 Source: bioRxiv

RNA viruses are proficient at switching host species, and evolving adaptations to exploit the new hosts cells efficiently. Surprisingly, SARS-CoV-2 has apparently required no significant adaptation to humans since the start of the COVID-19 pandemic, with no observed selective sweeps since genome sampling began. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses. In contrast, our analysis detects significant positive episodic diversifying selection acting on the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in ancestral hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor [~]1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection MESHD and evolution in bats without involvement of other species. Collectively our results demonstrate the progenitor of SARS-CoV-2 was capable of near immediate human-human transmission TRANS as a consequence of its adaptive evolutionary history in bats, not humans.

### SARS-CoV-2 infection MESHD, clinical features and outcome of COVID-19 in United Kingdom nursing homes

Authors: Neil SN Graham; Cornelia Junghans; Rawlda Downes; Catherine Sendall; Helen Lai; Annie McKirdy; Paul Elliott; Robert Howard; David Wingfield; Miles Priestman; Marta Ciechonska; Loren Cameron; Marko Storch; Michael Crone; Paul Freemont; Paul Randell; Robert McLaren; Nicola Lang; Shamez Ladhani; Frances Sanderson; David J Sharp

doi:10.1101/2020.05.19.20105460 Date: 2020-05-26 Source: medRxiv

Objectives: To understand SARS-Co-V-2 infection MESHD and transmission TRANS in UK nursing homes in order to develop preventive strategies for protecting the frail elderly TRANS residents. Design: An outbreak investigation. Setting: 4 nursing homes affected by COVID-19 outbreaks in central London. Participants: 394 residents and 70 staff in nursing homes. Interventions: Two point- prevalence SERO surveys one week apart where residents underwent SARS-CoV-2 testing and had relevant symptoms documented. Asymptomatic TRANS staff from three of the four homes were also offered SARS-CoV-2 testing. Main outcome measures: All-cause mortality, and mortality attributed to COVID-19 on death certificates. Prevalence SERO of SARS-CoV-2 infection MESHD and symptoms in residents and staff. Results: Overall, 26% (95% confidence interval 22 to 31) of residents died over the two-month period. All-cause mortality increased by 203% (95% CI 70 to 336). Systematic testing identified 40% (95% CI 35 to 46) of residents, of whom 43% (95% CI 34 to 52) were asymptomatic TRANS and 18% (95% CI 11 to 24) had atypical symptoms, as well as 4% (95% CI -1 to 9) of asymptomatic TRANS staff who tested positive for SARS-CoV-2. Conclusions: The SARS-CoV-2 outbreak was associated with a very high mortality rate in residents of nursing homes. Systematic testing of all residents and a representative sample of staff identified high rates of SARS-CoV-2 positivity across the four nursing homes, highlighting a potential for regular screening to prevent future outbreaks.

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