Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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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.

    Identification of novel antiviral drug combinations in vitro and tracking their development

    Authors: Aleksandr Ianevski; Rouan Yao; Svetlana Biza; Eva Zusinaite; Andres Mannik; Gaily Kivi; Anu Planken; Kristiina Kurg; Eva-Maria Tombak; Mart Ustav Jr.; Nastassia Shtaida; Evgeny Kulesskiy; Eunji Jo; Jaewon Yang; Hilde Lysvand; Kirsti Loseth; Valentyn Oksenych; Per Arne Aas; Tanel Tenson; Astra Vitkauskiene; Marc P. Windisch; Mona H Fenstad; Svein Arne Nordbo; Mart Ustav; Magnar Bjoras; Denis E Kainov

    doi:10.1101/2020.09.17.299933 Date: 2020-09-17 Source: bioRxiv

    Combination therapies have become a standard for the treatment for HIV and HCV infections MESHD. They are advantageous over monotherapies due to better efficacy and reduced toxicity MESHD, as well as the ability to prevent the development of resistant viral strains and to treat viral co-infections MESHD. Here, we identify several new synergistic combinations against emerging and re-emerging viral infections in vitro. We observed synergistic activity of nelfinavir with investigational drug EIDD-2801 and convalescent serum SERO against SARS-CoV-2 infection MESHD in human lung epithelial Calu-3 cells. We also demonstrated synergistic activity of vemurafenib combination with emetine, homoharringtonine, gemcitabine, or obatoclax against echovirus 1 infection MESHD in human lung epithelial A549 cells. We also found that combinations of sofosbuvir with brequinar and niclosamide were synergistic against HCV infection MESHD in hepatocyte derived Huh-7.5 cells, whereas combinations of monensin with lamivudine and tenofovir were synergistic against HIV-1 infection MESHD in human cervical TZM-bl cells. Finally, we present an online resource that summarizes novel and known antiviral drug combinations and their developmental status. Overall, the development of combinational therapies could have a global impact improving the preparedness and protection of the general population from emerging and re-emerging viral threats.

    Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness MESHD in Egypt at El-Demerdash tertiary hospitals

    Authors: Sara H.A.Agwa; Hesham Elghazaly; Sarah El-Nakeep; Ahmad Moustafa; Manal H El-Sayed; Hala Hafez; Samia abdo; Marwa Matboli; Maha Saad; Shaimaa M.Elsayed; Aya M.Abd Elsamie; Reham M.Darwish; Hoda ezz elarab; Fatma S. E. Ebeid; Sara Makkeyah; Mahmoud S El Meteini

    doi:10.21203/rs.3.rs-76216/v1 Date: 2020-09-11 Source: ResearchSquare

    Subject Area: SARS-CoV-2Purpose: COVID-19 is the most recent pandemic causing morbidity and mortality. Although a part of the pathogens causing SARI, it is unique in causing pulmonary thrombosis MESHD and lung fibrosis MESHD. Thus different management is needed. We aimed o explore the start of SARS-CoV-2 in preserved SARI samples to know the exact time of its emergence in our hospital, to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain.  To assess the clinical characteristics of the severe respiratory infection MESHD admitted to El-Demerdash hospitals in that same period from our own file reports.Methods: We conducted a retrospective cohort study among SARI patients who were admitted to Ain Shams university hospitals. preserved nasopharyngeal& oropharyngeal swabs from 333 SARI patients were used in SARS-CoV-2 detection by RT-Real time PCR. Moreover, whole-genome sequencing of SARS-CoV-2 positive samples was performed. Clinical characteristics of the SARI patients were analyzed in the same period to show the relation to morbidity and mortality.Results: The first case of SARS-CoV-2 was detected in a 6months aged TRANS female TRANS patient on mid-April 2020, B.1.1.7, clade GR. Co-infection MESHD (with both bacterial and viral) was most prevalent in pediatrics than adults TRANS, but mortality was higher in adults TRANS than pediatrics (18.1% versus 7.1%). ICU admission was higher in adults TRANS than in the pediatric group (65% versus 12.8%). Co-morbidities were associated with higher mortality and more severe infection HP infection MESHD. The most common bacterial infection MESHD in both adults TRANS and pediatrics was Klebsiella pneumoniae MESHD pneumoniae HP, followed by Staphylococcus aureus and Streptococcus pneumoniae HP. Conclusion: COVID-19 didn’t start till mid-April in the Egyptian hospitals as remarked by this tertiary hospital’s data. Co-infection MESHD is the most prevalent in children TRANS and further research is needed in this area.

    Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness MESHD in Egypt at El-Demerdash tertiary hospitals

    Authors: Sara H.A.Agwa; Hesham Elghazaly; Sarah El-Nakeep; Ahmad Moustafa; Manal H El-Sayed; Hala Hafez; Samia abdo; Marwa Matboli; Maha Saad; Shaimaa M.Elsayed; Aya M.Abd Elsamie; Reham M.Darwish; Hoda ezz elarab; Fatma S. E. Ebeid; Sara Makkeyah; Mahmoud S El Meteini

    doi:10.21203/rs.3.rs-76216/v2 Date: 2020-09-11 Source: ResearchSquare

    Purpose: COVID-19 is the most recent pandemic causing morbidity and mortality. Although a part of the pathogens causing SARI, it is unique in causing pulmonary thrombosis MESHD and lung fibrosis MESHD. Thus different management is needed. We aimed o explore the start of SARS-CoV-2 in preserved SARI samples to know the exact time of its emergence in our hospital, to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain.  To assess the clinical characteristics of the severe respiratory infection MESHD admitted to El-Demerdash hospitals in that same period from our own file reports.Methods: We conducted a retrospective cohort study among SARI patients who were admitted to Ain Shams university hospitals. preserved nasopharyngeal& oropharyngeal swabs from 333 SARI patients were used in SARS-CoV-2 detection by RT-Real time PCR. Moreover, whole-genome sequencing of SARS-CoV-2 positive samples was performed. Clinical characteristics of the SARI patients were analyzed in the same period to show the relation to morbidity and mortality.Results: The first case of SARS-CoV-2 was detected in a 6months aged TRANS female TRANS patient on mid-April 2020, B.1.1.7, clade GR. Co-infection MESHD (with both bacterial and viral) was most prevalent in pediatrics than adults TRANS, but mortality was higher in adults TRANS than pediatrics (18.1% versus 7.1%). ICU admission was higher in adults TRANS than in the pediatric group (65% versus 12.8%). Co-morbidities were associated with higher mortality and more severe infection HP infection MESHD. The most common bacterial infection MESHD in both adults TRANS and pediatrics was Klebsiella pneumoniae MESHD pneumoniae HP, followed by Staphylococcus aureus and Streptococcus pneumoniae HP. Conclusion: COVID-19 didn’t start till mid-April in the Egyptian hospitals as remarked by this tertiary hospital’s data. Co-infection MESHD is the most prevalent in children TRANS and further research is needed in this area.

    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

    BackgroundIn response to the recent information about the outbreak of Kawasaki disease MESHD ( KD MESHD) in children TRANS connected to SARS-Cov-2 pandemic, we would like to present a group of six patients hospitalized from March to May 2020 with an inflammatory disease similar to KD MESHD. Findings There were four girls and two boys, aged TRANS from 15 months to 16 years. They all presented with fever HP fever MESHD lasting at least five days, irritability HP irritability MESHD, bilateral nonexudative conjunctivitis HP conjunctivitis MESHD, lymphadenopathy, mucus membrane changes, rash MESHD, edema HP edema MESHD.Neither the patients nor the other members of the patients' households had a positive history of COVID-19 infection MESHD. None of the six children TRANS had a positive PCR result for SARS-CoV-2 or a positive results for antibodies to SARS-CoV-2 SERO. All patients received empiric antibiotic therapy. Four patients were diagnosed with KD MESHD. Three children TRANS received standard treatment. One boy did not respond and received an additional 14-days course of methylprednisolone.In two girls, the diagnosis of KD MESHD was not made. All patients survived ConclusionFinding a correlation with the Covid-19 pandemic is difficult regarding the situation in our country. According to ECDC, in May 2020 Poland wass still before the peak of the epidemy. The intention of this article is to report that increased hospitalization of children TRANS with the inflammatory syndrome MESHD is also observed in countries with low levels of transmission TRANS of the SARS-Cov-2 virus. Our observation may broaden the knowledge of new inflammatory syndrome MESHD, which is not necessarily caused by SARS-Cov-2 but may be worsened by co-infection MESHD.

    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.

    Ocular findings and retinal involvement in COVID-19 pneumonia HP pneumonia MESHD patients: A cross-sectional study in an Italian referral centre

    Authors: Maria Pia Pirraglia; Giancarlo Ceccarelli; Alberto Cerini; Giacomo Visioli; Gabriella d'Ettorre; Claudio Maria Mastroianni; Francesco Pugliese; Alessandro Lambiase; Magda Gharbiya

    doi:10.21203/rs.3.rs-48240/v1 Date: 2020-07-23 Source: ResearchSquare

    Background: changes in immune and coagulation systems and possible viral spread through blood SERO-brain barrier have been described in SARS-CoV-2 infection MESHD. In this study, we evaluate the possible retinal involvement and ocular findings in severe COVID-19 pneumonia HP pneumonia MESHD patients.  Methods: a cross sectional study was conducted on 46 patients affected by severe COVID-19 who were hospitalized in one Intensive Care Unit (ICU) and in two Infectious Diseases wards, including a bedside eye screening, corneal sensitivity SERO assessment and retinography. Results: a total of 43 SARS-CoV-2 positive pneumonia MESHD pneumonia HP patients affected with COVID-19 pneumonia HP pneumonia MESHD were included, 25 males TRANS and 18 females TRANS, with a median age TRANS of 70 [IQR 59-78]. Except for one patient with unilateral posterior chorioretinitis HP of opportunistic origin, of whom aqueous tap was negative for SARS-CoV-2, no further retinal manifestation related to COVID-19 infection MESHD was found in our cohort. We found 3 patients (7%) with bilateral conjunctivitis MESHD conjunctivitis HP in whom PCR analysis on conjunctival swab provided negative results for SARS-CoV-2. No alterations of corneal sensitivity SERO were found.Conclusion: we demonstrated the absence of retinal involvement in SARS-CoV-2 pneumonia MESHD pneumonia HP patients. Ophthalmologic evaluation in COVID-19, particularly in patients hospitalized in an ICU setting, may be useful to reveal systemic co-infections MESHD infections by opportunistic HP pathogens. 

    A Preceding Low-virulence Strain Pandemic Inducing Immunity Against COVID-19

    Authors: Hagai Perets; Ruth Perets

    id:202007.0352/v1 Date: 2020-07-16 Source: Preprints.org

    Abstract The COVID-19 pandemic is thought to began in Wuhan, China in December 2019. Mobility analysis identified East-Asia and Oceania countries to be highly-exposed to COVID-19 spread, consistent with the earliest spread occurring in these regions. However, here we show that while a strong positive correlation between case-numbers and exposure level could be seen early-on as expected, at later times the infection-level is found to be negatively correlated with exposure-level. Moreover, the infection MESHD level is positively correlated with the population size, which is puzzling since it has not reached the level necessary for population-size to affect infection-level through herd immunity. These issues are resolved if a low-virulence Corona-strain (LVS) began spreading earlier in China outside of Wuhan, and later globally, providing immunity from the later appearing high-virulence strain (HVS). Following its spread into Wuhan, cumulative mutations gave rise to the emergence of an HVS, known as SARS-CoV-2, starting the COVID-19 pandemic. We model the co-infection MESHD by an LVS and an HVS, and show that it can explain the evolution of the COVID-19 pandemic and the non-trivial dependence on the exposure level to China and the population-size in each country. We find that the LVS began its spread a few months before the onset of the HVS, and that its spread doubling-time is ∼ 1.59 ± 0.17 times slower than the HVS. Although more slowly spreading, its earlier onset allowed the LVS to spread globally before the emergence of the HVS. In particular, in countries exposed earlier to the LVS and/or having smaller population-size, the LVS could achieve herd-immunity earlier, and quench the later-spread HVS at earlier stages. We find our two-parameter (the spread-rate and the initial onset time of the LVS) can accurately explain the current infection levels (R^2=0.74; correlation p-value (p) of 5x10^-13 ). Furthermore, countries exposed early should have already achieved herd-immunity. We predict that in those countries cumulative infection levels could rise by no more than 2-3 times the current level through local-outbreaks, even in the absence of any containment measures. We suggest several tests and predictions to further verify the double-strain co-infection MESHD model and discuss the implications of identifying the LVS.

    Optimized Laboratory Detection Strategy for COVID-19 Patients Reduces the Rate of Missed Diagnosis

    Authors: Wenjiao Chang; Yuru Shi; Yingjie Qi; Jiaxing Liu; Ting Liu; Zhaowu Chen; Dongfeng Liu; Ming Yin; Jing Xu; Yun Yang; Jing Ge; Shu Zhu; Yong Gao; Xiaoling Ma

    doi:10.21203/rs.3.rs-42485/v1 Date: 2020-07-13 Source: ResearchSquare

    Background: Novel coronavirus pneumonia MESHD pneumonia HP (NCP) is an emerging, highly contagious community acquired pneumonia HP pneumonia MESHD (CAP) caused by severe acute SARS-CoV-2. Nucleic acid test currently played a crucial role in diagnosis of suspected COVID-19 patients. However, a high false-negative rate of this “gold standard” test has been reported and posed a major setback in blocking the spread of the virus. We here aim to describe an optimized laboratory detection strategy to reduce the false negative rate. Methods: Suspected NCP patients were asked to collect both coughed HP up specimen and pharyngeal swab. Samples from the same patient were mixed and tested at a single pool. SARS-CoV-2 was then detected by real-time RT-PCR using two different detection kits. Only if both results were negative was the test reported as negative. The patients will be excluded after two consecutive negative tests at 24 hour intervals. We also used multiplex PCR to detect 13 common respiratory tract pathogens (RTP). Results: Using this strategy, we confirmed 85 SARS-CoV-2 infections MESHD from 181 suspected patients, and 94.12% of patients were positive in the first test. The 96 excluded patients were followed up, and no additional NCP was found. We also found that 31.25% patients in 96 non-NCP patients were infected MESHD with at least one RTP that may cause CAP. Conclusion: Our studies suggest that dual reagents screening with pooled coughed HP up specimen and pharyngeal swab samples reduced the false negative rate of nucleic acid testing. During the epidemic of NCP in Anhui province, there was a certain proportion of infection and co-infection MESHD of other common pathogens of CAP. In comparison with SARS-CoV-2 detection alone, combining multiple pathogen detection reduces the rate of miss diagnosis.

    A preceding low-virulence strain pandemic inducing immunity against COVID-19

    Authors: Hagai Perets; Ruth Perets

    doi:10.21203/rs.3.rs-41098/v1 Date: 2020-07-11 Source: ResearchSquare

    The COVID-19 pandemic is thought to began in Wuhan, China in December 2019. Mobility analysis identified East-Asia and Oceania countries to be highly-exposed to COVID-19 spread, consistent with the earliest spread occurring in these regions. However, here we show that while a strong positive correlation between case-numbers and exposure level could be seen early-on as expected, at later times the infection-level is found to be negatively correlated with exposure-level. Moreover, the infection MESHD level is positively correlated with the population size, which is puzzling since it has not reached the level necessary for population-size to affect infection-level through herd immunity. These issues are resolved if a low-virulence Corona-strain (LVS) began spreading earlier in China outside of Wuhan, and later globally, providing immunity from the later appearing high-virulence strain (HVS). Following its spread into Wuhan, cumulative mutations gave rise to the emergence of an HVS, known as SARS-CoV-2, starting the COVID-19 pandemic. We model the co-infection MESHD by an LVS and an HVS and show that it can explain the evolution of the COVID-19 pandemic and the non-trivial dependence on the exposure level to China and the population-size in each country. We find that the LVS began its spread a few months before the onset of the HVS MESHD and that its spread doubling-time is \sim1.59\pm0.17 times slower than the HVS. Although more slowly spreading, its earlier onset allowed the LVS to spread globally before the emergence of the HVS. In particular, in countries exposed earlier to the LVS and/or having smaller population-size, the LVS could achieve herd-immunity earlier, and quench the later-spread HVS at earlier stages. We find our two-parameter (the spread-rate and the initial onset time of the LVS) can accurately explain the current infection levels (R^2=0.74); p-value (p) of 5.2x10^-13). Furthermore, countries exposed early should have already achieved herd-immunity. We predict that in those countries cumulative infection levels could rise by no more than 2-3 times the current level through local-outbreaks, even in the absence of any containment measures. We suggest several tests and predictions to further verify the double-strain co-infection MESHD model and discuss the implications of identifying the LVS.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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