Corpus overview


MeSH Disease

Human Phenotype


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    Characterization of Microbial Co-infections MESHD infections in the Respiratory Tract HP of hospitalized COVID-19 patients

    Authors: Huanzi Zhong; Yanqun Wang; Zhun Shi; Lu Zhang; Huahui Ren; Weiqun He; Zhaoyong Zhang; Airu Zhu; Jingxian Zhao; Fei Xiao; Fangming Yang; Tianzhu Liang; Feng Ye; Bei Zhong; Shicong Ruan; Mian Gan; Jiahui Zhu; Fang Li; Fuqiang Li; Daxi Wang; Jiandong Li; Peidi Ren; Shida Zhu; Huanming Yang; Jian Wang; Karsten Kristiansen; Hein M Tun; Weijun Chen; Nanshan Zhong; Xun Xu; Yi-min Li; Junhua LI; Jincun Zhao

    doi:10.1101/2020.07.02.20143032 Date: 2020-07-05 Source: medRxiv

    Summary Background Severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) has caused a global pandemic of Coronavirus disease MESHD 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Method Between January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection MESHD rates, the prevalence SERO and abundance of microbial communities in these COVID-19 patients were determined. Findings Notably, respiratory microbial co-infections MESHD were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections MESHD were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections MESHD with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis MESHD were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death MESHD one month after ICU admission. Interpretation Our findings identified distinct patterns of co-infections MESHD with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections MESHD are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2. Funding National Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease MESHD in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.

    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:

    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.

    Prevalence SERO, clinical characteristics and treatment outcomes of HIV MESHD and SARS-CoV-2 co-infection MESHD: a systematic review and meta-analysis

    Authors: Joseph Baruch Baluku; Ronald Olum; Curthbert Agolor; Josephine Nakakande; Laura Russell; Felix Bongomin; Jane Nakaweesi

    doi:10.1101/2020.05.31.20118497 Date: 2020-06-03 Source: medRxiv

    Objectives: To determine the prevalence SERO, clinical characteristics and outcomes of HIV MESHD and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infection MESHD. Methods: We searched Medline, Embase, Cochrane and Web of Science databases and grey literature for studies reporting epidemiological and clinical data of patients with HIV MESHD and SARS-CoV-2 co-infection MESHD. Eligible studies were all observational or interventional studies and commentaries in English language that reported patient data on HIV/SARS-CoV-2 co-infection MESHD. We used random effect meta-analysis to determine the pooled prevalence SERO and mortality. Results: Of the 17 eligible studies, there were 3 retrospective cohorts, 1 survey, 5 case series, 7 case reports and 1 commentary that reported on a total of 146 HIV infected MESHD individuals. The pooled prevalence SERO of HIV among individuals with SARS-CoV-2 infection MESHD was 1.0% (95% CI: 0.0 - 3.0, I2 = 79.3%, p=0.01), whereas the prevalence SERO of SARS-CoV-2 among HIV patients was 0.68% (95% CI: 0.34 - 1.34). There were 110 (83.8%) HIV MESHD/ SARS-CoV-2 co-infected males MESHD males TRANS, and the age TRANS (range) of the co-infected MESHD was 30 - 60 years. A total of 129 (97.0%) were anti-retroviral therapy experienced, and 113 (85.6%) had a suppressed HIV viral load. The CD4 count (range) was 298 - 670 cells/mm3 (n = 107). The commonest symptoms were fever HP fever MESHD (73.5%, n=75) and cough HP (57.8%, n = 59). Sixty-two (65.3%) patients had at least one other comorbid condition, of which hypertension HP hypertension MESHD (26.4%, n = 38) was the commonest. Chest radiological imaging abnormalities were found in 46 (54.1%) cases. Twenty-eight cases (56.0%) were reported as mild. Recovery occurred in 120 (88.9%) cases, and the pooled mortality was 9% (95% CI: 3.0 - 15.0, I2 = 25.6%, p =0.24). Conclusion: The prevalence SERO of HIV/SARS-CoV-2 co-infection MESHD was low. The clinical characteristics and outcomes of HIV/SARS-CoV-2 co-infection MESHD are comparable to those reported among HIV negative SARS-CoV-2 cases.

    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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MeSH Disease
Human Phenotype

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