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2.
Inflamm Bowel Dis ; 26(9): 1306-1314, 2020 08 20.
Article in English | MEDLINE | ID: covidwho-684619

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has a direct impact on the gastrointestinal system, as up to 50% of fecal samples from coronavirus disease 2019 (COVID-19) patients contain detectable viral RNA despite a negative rhino-pharyngeal swab. This finding, together with an intestinal expression of angiotensin conversion enzyme 2 protein, suggests a possible fecal-oral transmission for SARS-CoV-2. Furthermore, gastrointestinal (GI) symptoms are common in COVID-19 patients including watery diarrhea, vomiting-particularly in children-nausea, and abdominal pain. Pathogenesis of SARS-CoV-2 infection presents significant similarities to those of some immune-mediated diseases, such as inflammatory bowel diseases or rheumatoid arthritis, leading to the hypothesis that targeted therapies used for the treatment of immune-mediated disease could be effective to treat (and possibly prevent) the main complications of COVID-19. In this review, we synthesize the present and future impact of SARS-CoV-2 infection on the gastrointestinal system and on gastroenterology practice, hypothesizing a potential role of the "gut-lung axis" and perhaps of the gut and lung microbiota into the interindividual differential susceptibility to COVID-19 19 disease. Finally, we speculate on the reorganization of outpatient gastroenterology services, which need to consider, among other factors, the major psychological impact of strict lockdown measures on the whole population.


Subject(s)
Betacoronavirus , Coronavirus Infections/complications , Gastrointestinal Diseases/virology , Pneumonia, Viral/complications , Coronavirus Infections/virology , Feces/virology , Gastrointestinal Tract/virology , Humans , Pandemics , Pneumonia, Viral/virology , RNA, Viral/analysis
3.
J Clin Microbiol ; 58(9)2020 08 24.
Article in English | MEDLINE | ID: covidwho-636249

ABSTRACT

The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The viral antigen was detected by a rapid antigen immunochromatographic assay. Of the 103 samples, viral RNA was detected in 50.5 to 81.6% of the specimens by molecular diagnostic tests, and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at significantly higher percentages (65.6 to 93.4%) in specimens collected within 9 days of symptom onset than in specimens collected after at least 10 days of symptoms (22.2 to 66.7%) and in specimens collected from asymptomatic patients (40.0 to 66.7%). Self-collected saliva is an alternative specimen option for diagnosing COVID-19. The RT-qPCR LDT, a cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed sufficient sensitivities in clinical use to be selectively used in clinical settings and facilities. The rapid antigen test alone is not recommended for an initial COVID-19 diagnosis because of its low sensitivity.


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Immunoassay , Nucleic Acid Amplification Techniques , Pneumonia, Viral/diagnosis , Saliva/virology , Adolescent , Adult , Aged , Aged, 80 and over , Antigens, Viral/analysis , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Clinical Laboratory Techniques/statistics & numerical data , Female , Humans , Immunoassay/methods , Immunoassay/standards , Immunoassay/statistics & numerical data , Male , Middle Aged , Nucleic Acid Amplification Techniques/methods , Nucleic Acid Amplification Techniques/standards , Nucleic Acid Amplification Techniques/statistics & numerical data , Pandemics , RNA, Viral/analysis , RNA, Viral/genetics , Sensitivity and Specificity , Specimen Handling , Young Adult
4.
J Dent Res ; 99(10): 1199-1205, 2020 09.
Article in English | MEDLINE | ID: covidwho-626677

ABSTRACT

This study aimed to determine if sampling of oropharyngeal secretions (OSs) helps improves detection of SARS-CoV-2 RNA by nucleic acid amplification testing of potential patients with COVID-19. The first prospective study consisted of 75 patients with COVID-19 who were ready for discharge and who had 2 consecutive negative results per nucleic acid amplification testing (NAAT) of viral samples retrieved with nasopharyngeal swabs (NPSs). Because of detection of potential false negatives in that cohort, the NAAT results of paired OS and NPS samples from 50 additional recruits with COVID-19 during their recovery stage were used in a second prospective study to compare the diagnostic values of the 2 viral RNA sampling methods. For identification of the frequency of inconsistency between the sampling methods, the McNemar's test was used for difference analysis and the kappa statistic for consistency analysis. OSs obtained from 2 of the 75 participants in the first study yielded positive results for SARS-CoV-2 nucleic acid. Both were male and aged >60 y. Subsequent chemiluminescence enzyme immunoassays indicated that they were positive for the SARS-CoV-2 IgM and IgG antibodies. For parallel NAAT of OS and NPS samples in the second study, McNemar's test indicated that the difference between the frequencies of inconsistent parts of OS and NPS was statistically significant (P = 0.021). Cohen's kappa coefficient for OS and NPS was 0.244, which is indicative of fair consistency. The NPS test has a risk of sending home more patients (59%) who still have the infection, while the OS test will make such an error in fewer patients (14%). Although OS sampling improves the accuracy of SARS-CoV-2 nucleic acid testing, it has to be emphasized that this conclusion is based on a very small sample size. Detection of viral RNA from a patient's secretions is not confirmative of viral infectivity.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Oropharynx/virology , Pneumonia, Viral/diagnosis , Clinical Laboratory Techniques , Humans , Male , Middle Aged , Pandemics , Prospective Studies , RNA, Viral/isolation & purification
5.
Genome Med ; 12(1): 57, 2020 06 30.
Article in English | MEDLINE | ID: covidwho-618232

ABSTRACT

BACKGROUND: COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-CoV-2 directly from clinical samples have not been completely tackled, i.e., sequencing samples with low viral load often results in insufficient viral reads for analyses. METHODS: We applied a novel multiplex PCR amplicon (amplicon)-based and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of SARS-CoV-2 from serials dilutions of a cultured isolate, and eight clinical samples covering a range of sample types and viral loads. We also examined and compared the sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. RESULTS: We demonstrated that both amplicon and capture methods efficiently enriched SARS-CoV-2 content from clinical samples, while the enrichment efficiency of amplicon outran that of capture in more challenging samples. We found that capture was not as accurate as meta and amplicon in identifying between-sample variations, whereas amplicon method was not as accurate as the other two in investigating within-sample variations, suggesting amplicon sequencing was not suitable for studying virus-host interactions and viral transmission that heavily rely on intra-host dynamics. We illustrated that meta uncovered rich genetic information in the clinical samples besides SARS-CoV-2, providing references for clinical diagnostics and therapeutics. Taken all factors above and cost-effectiveness into consideration, we proposed guidance for how to choose sequencing strategy for SARS-CoV-2 under different situations. CONCLUSIONS: This is, to the best of our knowledge, the first work systematically investigating inter- and intra-individual variations of SARS-CoV-2 using amplicon- and capture-based whole-genome sequencing, as well as the first comparative study among multiple approaches. Our work offers practical solutions for genome sequencing and analyses of SARS-CoV-2 and other emerging viruses.


Subject(s)
Betacoronavirus/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing/methods , Whole Genome Sequencing/methods , Coronavirus Infections , Genetic Variation/genetics , Host-Pathogen Interactions/genetics , Humans , Multiplex Polymerase Chain Reaction/methods , Pandemics , Pneumonia, Viral , RNA, Viral/genetics
6.
J Virol ; 94(15)2020 07 16.
Article in English | MEDLINE | ID: covidwho-762192

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe acute respiratory disease in humans. MERS-CoV strains from early epidemic clade A and contemporary epidemic clade B have not been phenotypically characterized to compare their abilities to infect cells and mice. We isolated the clade B MERS-CoV ChinaGD01 strain from a patient infected during the South Korean MERS outbreak in 2015 and compared the phylogenetics and pathogenicity of MERS-CoV EMC/2012 (clade A) and ChinaGD01 (clade B) in vitro and in vivo Genome alignment analysis showed that most clade-specific mutations occurred in the orf1ab gene, including mutations that were predicted to be potential glycosylation sites. Minor differences in viral growth but no significant differences in plaque size or sensitivity to beta interferon (IFN-ß) were detected between these two viruses in vitro ChinaGD01 virus infection induced more weight loss and inflammatory cytokine production in human DPP4-transduced mice. Viral titers were higher in the lungs of ChinaGD01-infected mice than with EMC/2012 infection. Decreased virus-specific CD4+ and CD8+ T cell numbers were detected in the lungs of ChinaGD01-infected mice. In conclusion, MERS-CoV evolution induced changes to reshape its pathogenicity and virulence in vitro and in vivo and to evade adaptive immune response to hinder viral clearance.IMPORTANCE MERS-CoV is an important emerging pathogen and causes severe respiratory infection in humans. MERS-CoV strains from early epidemic clade A and contemporary epidemic clade B have not been phenotypically characterized to compare their abilities to infect cells and mice. In this study, we showed that a clade B virus ChinaGD01 strain caused more severe disease in mice, with delayed viral clearance, increased inflammatory cytokines, and decreased antiviral T cell responses, than the early clade A virus EMC/2012. Given the differences in pathogenicity of different clades of MERS-CoV, periodic assessment of currently circulating MERS-CoV is needed to monitor potential severity of zoonotic disease.


Subject(s)
Coronavirus Infections/virology , Genotype , Host-Pathogen Interactions , Middle East Respiratory Syndrome Coronavirus/physiology , Adult , Animals , Disease Models, Animal , Genome, Viral , Host-Pathogen Interactions/immunology , Humans , Interferon Type I/pharmacology , Male , Mice , Middle East Respiratory Syndrome Coronavirus/classification , Middle East Respiratory Syndrome Coronavirus/isolation & purification , Middle East Respiratory Syndrome Coronavirus/pathogenicity , Phylogeny , RNA, Viral , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Virulence , Virus Replication/drug effects , Virus Replication/genetics , Whole Genome Sequencing
7.
J Clin Microbiol ; 58(9)2020 08 24.
Article in English | MEDLINE | ID: covidwho-751568

ABSTRACT

The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription-loop-mediated isothermal amplification (RT-LAMP). The viral antigen was detected by a rapid antigen immunochromatographic assay. Of the 103 samples, viral RNA was detected in 50.5 to 81.6% of the specimens by molecular diagnostic tests, and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at significantly higher percentages (65.6 to 93.4%) in specimens collected within 9 days of symptom onset than in specimens collected after at least 10 days of symptoms (22.2 to 66.7%) and in specimens collected from asymptomatic patients (40.0 to 66.7%). Self-collected saliva is an alternative specimen option for diagnosing COVID-19. The RT-qPCR LDT, a cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed sufficient sensitivities in clinical use to be selectively used in clinical settings and facilities. The rapid antigen test alone is not recommended for an initial COVID-19 diagnosis because of its low sensitivity.


Subject(s)
Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Immunoassay , Nucleic Acid Amplification Techniques , Pneumonia, Viral/diagnosis , Saliva/virology , Adolescent , Adult , Aged , Aged, 80 and over , Antigens, Viral/analysis , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Clinical Laboratory Techniques/statistics & numerical data , Female , Humans , Immunoassay/methods , Immunoassay/standards , Immunoassay/statistics & numerical data , Male , Middle Aged , Nucleic Acid Amplification Techniques/methods , Nucleic Acid Amplification Techniques/standards , Nucleic Acid Amplification Techniques/statistics & numerical data , Pandemics , RNA, Viral/analysis , RNA, Viral/genetics , Sensitivity and Specificity , Specimen Handling , Young Adult
8.
Mymensingh Med J ; 29(3): 596-600, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-746340

ABSTRACT

There is a new public health problem around the world with the emergence and spread of 2019 novel corona virus (2019-nCoV). The disease "coronavirus disease 2019" (COVID-19) was caused by SARS-CoV-2. As virus isolates are unavailable so the public laboratories are now facing a challenge for detecting the virus because there is growing evidence of the outbreak which is more widespread than initially thought. We aimed here to discuss about the current diagnostic methodology for detecting the SARS-CoV-2 in health laboratories. Here we use the Novel Corona virus (2019-nCoV) Nucleic Acid Diagnostic Kit (PCR-Fluorescence Probing) which is a real time reverse transcription polymerase chain reaction (rRT-PCR) test. A total of 230 samples in the department of microbiology, Mymensingh Medical College from 1st, April 2020 were selected for this study. Among them 20(8.69%) were positive for SARS CoV-2 and remaining were negative. Among the positive samples 55% could amplify both the ORF 1ab and N genes. The single gene ORF 1ab or N was positive in 15% and 30% cases respectively. The Ct values (<38) of ORF 1ab gene indicated by FAM dye was 92.8% and N gene curve indicated by ROX dye was 100%. The presence of IC gene curve with Ct values (<38) indicated by CY5 dye among the positives were 70% and 100% in negatives. The Ct values (38-40) of IC (CY5) among the positives were 15%. The present study demonstrates the enormous response capacity of the study kit for detecting SARS-CoV-2 within the laboratories in Bangladesh.


Subject(s)
Coronavirus Infections/diagnosis , Coronavirus/genetics , Coronavirus/isolation & purification , Pandemics , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/methods , Bangladesh , Betacoronavirus , Clinical Laboratory Techniques/methods , Coronavirus Infections/epidemiology , Humans , Pneumonia, Viral/epidemiology , RNA, Viral/analysis
9.
J Zhejiang Univ Sci B ; 21(9): 749-751, 2020.
Article in English | MEDLINE | ID: covidwho-745668

ABSTRACT

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was found initially in Wuhan, China in early December 2019. The pandemic has spread to 216 countries and regions, infecting more than 23310 000 people and causing over 800 000 deaths globally by Aug. 24, 2020, according to World Health Organization (https://www.who.int/emergencies/diseases/ novel-coronavirus-2019). Fever, cough, and dyspnea are the three common symptoms of the condition, whereas the conventional transmission route for SARS-CoV-2 is through droplets entering the respiratory tract. To date, infection control measures for COVID-19 have been focusing on the involvement of the respiratory system. However, ignoring potential faecal transmission and the gastrointestinal involvement of SARS-CoV-2 may result in mistakes in attempts to control the pandemic.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/transmission , Coronavirus Infections/virology , Feces/virology , Gastrointestinal Diseases/virology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Betacoronavirus/genetics , China/epidemiology , Coronavirus Infections/epidemiology , Environmental Microbiology , Humans , Models, Biological , Pandemics , Pneumonia, Viral/epidemiology , RNA, Viral/analysis , RNA, Viral/genetics , Virus Shedding
10.
Biomed Res Int ; 2020: 2721381, 2020.
Article in English | MEDLINE | ID: covidwho-744899

ABSTRACT

Introduction: Emergency department (ED) triage regarding infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is challenging. During the coronavirus disease 2019 (COVID-19) outbreak in Germany, the diagnostic outcomes of critically ill patients admitted to the resuscitation room in the ED of our academic 754-bed hospital should be analyzed. Methods: All resuscitation room patients between March 1st and April 15th 2020 were included in this retrospective study. Every patient with suspicion of SARS-CoV-2 infection received a pharyngeal swab for real-time polymerase chain reaction (rt-PCR), divided in the clinical subgroups of "highly suspicious for COVID-19" and "COVID-19 as differential diagnosis." All respiratory and infectious symptoms were included as at least "differential diagnosis" as an expanded suspicion strategy. Results: Ninety-five patients were included (trauma n = 14, critically ill n = 81). Of 3 highly suspicious patients, 2 had rt-PCR positive pharyngeal swabs. In 39 patients, COVID-19 was defined as differential diagnosis, and 3 were positive for SARS-CoV-2. Of them, pharyngeal swabs were positive in 1 case, while in 2 cases, only tracheal fluid was rt-PCR positive while the pharyngeal swabs were negative. In one of these 2 cases, chest computed tomography (CT) was also negative for ground-glass opacities but showed a pulmonary abscess and pulmonary embolism. Conclusion: We recommend an expanded suspicion strategy for COVID-19 due to unexpected diagnostic outcomes. Personal protective equipment should be used in every resuscitation room operation due to unexpected cases and initial knowledge gaps. Furthermore, tracheal fluid should be tested for SARS-CoV-2 in every intubated patient due to cases with negative pharyngeal swabs and negative chest CT.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Aged , Aged, 80 and over , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/epidemiology , Critical Illness , Diagnosis, Differential , Disease Outbreaks , Emergency Service, Hospital , False Negative Reactions , Female , Germany/epidemiology , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/epidemiology , RNA, Viral/genetics , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , Resuscitation , Retrospective Studies , Tomography, X-Ray Computed , Triage
11.
BMC Infect Dis ; 20(1): 644, 2020 Sep 01.
Article in English | MEDLINE | ID: covidwho-740367

ABSTRACT

BACKGROUND: To explore the clinical features and CT findings of clinically cured coronavirus disease 2019 (COVID-19) patients with viral RNA positive anal swab results after discharge. METHODS: Forty-two patients with COVID-19 who were admitted to Yongzhou Central Hospital, Hunan, China, between January 20, 2020, and March 2, 2020, were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using anal swab viral RT-PCR. In this report, we present the clinical characteristics and chest CT features of six patients with positive anal swab results and compare the clinical, laboratory, and CT findings between the positive and negative groups. RESULTS: The anal swab positivity rate for SARS-CoV-2 RNA in discharged patients was 14.3% (6/42). All six patients were male. In the positive group, 40% of the patients (2/5) had a positive stool occult blood test (OBT), but none had diarrhea. The median duration of fever and major symptoms (except fever) in the positive patients was shorter than that of the negative patients (1 day vs. 6 days, 4.5 days vs. 10.5 days, respectively). The incidence of asymptomatic cases in the positive group (33.3%) was also higher than that of the negative group (5.6%). There were no significant differences in the CT manifestation or evolution of the pulmonary lesions between the two groups. CONCLUSION: In our case series, patients with viral RNA positive anal swabs did not exhibit gastrointestinal symptoms, and their main symptoms disappeared early. They had similar CT features to the negative patients, which may be easier to be ignored. A positive OBT may indicate gastrointestinal damage caused by SARS-CoV-2 infection.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnostic imaging , Patient Discharge/statistics & numerical data , Pneumonia, Viral/diagnostic imaging , RNA, Viral/analysis , Severe Acute Respiratory Syndrome/diagnostic imaging , Adolescent , Adult , Aged , Anal Canal/virology , Betacoronavirus/genetics , Child , Child, Preschool , China/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Fever , Hospitalization , Hospitals , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Reverse Transcriptase Polymerase Chain Reaction , Severe Acute Respiratory Syndrome/epidemiology , Severe Acute Respiratory Syndrome/virology , Tomography, X-Ray Computed , Young Adult
12.
Ann Ital Chir ; 91: 235-238, 2020.
Article in English | MEDLINE | ID: covidwho-739563

ABSTRACT

The present pandemic caused by the SARS COV-2 coronavirus is still ongoing, although it is registered a slowdown in the spread for new cases. The main environmental route of transmission of SARS-CoV-2 is through droplets and fomites or surfaces, but there is a potential risk of virus spread also in smaller aerosols during various medical procedures causing airborne transmission. To date, no information is available on the risk of contagion from the peritoneal fluid with which surgeons can come into contact during the abdominal surgery on COVID-19 patients. We have investigated the presence of SARS-CoV-2 RNA in the peritoneal cavity of patients affected by COVID-19, intraoperatively and postoperatively. KEY WORDS: Covid-19, Laparotomy, Surgery.


Subject(s)
Ascitic Fluid/virology , Betacoronavirus/isolation & purification , Coronavirus Infections/transmission , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Intestinal Perforation/surgery , Laparotomy , Pandemics , Pneumonia, Viral/transmission , Sigmoid Diseases/surgery , Viremia/transmission , Aerosols , Aged, 80 and over , Coronavirus Infections/blood , Coronavirus Infections/complications , Coronavirus Infections/prevention & control , Cross-Sectional Studies , Diverticulum/complications , Fatal Outcome , Female , Humans , Intestinal Perforation/blood , Intestinal Perforation/complications , Intestinal Perforation/virology , Intraoperative Period , Nasopharynx/virology , Pandemics/prevention & control , Pneumonia, Viral/blood , Pneumonia, Viral/complications , Pneumonia, Viral/prevention & control , Postoperative Period , Prospective Studies , RNA, Viral/isolation & purification , Risk , Serum/virology , Sigmoid Diseases/blood , Sigmoid Diseases/complications , Sigmoid Diseases/virology , Viremia/virology
13.
Zhonghua Liu Xing Bing Xue Za Zhi ; 41(8): 1220-1224, 2020 Aug 10.
Article in Chinese | MEDLINE | ID: covidwho-739002

ABSTRACT

Objective: To understand the epidemiological characteristics of COVID-19 monitoring cases in Yinzhou district based on health big data platform to provide evidence for the construction of COVID-19 monitoring system. Methods: Data on Yinzhou COVID-19 daily surveillance were collected. Information on patients' population classification, epidemiological history, COVID-19 nucleic acid detection rate, positive detection rate and confirmed cases monitoring detection rate were analyzed. Results: Among the 1 595 COVID-19 monitoring cases, 79.94% were community population and 20.06% were key population. The verification rate of monitoring cases was 100.00%. The total percentage of epidemiological history related to Wuhan city or Hubei province was 6.27% in total, and was 2.12% in community population and 22.81% in key population (P<0.001). The total COVID-19 nucleic acid detection rate was 18.24% (291/1 595), and 53.00% in those with epidemiological history and 15.92% in those without (P<0.001).The total positive detection rate was 1.72% (5/291) and the confirmed cases monitoring detection rate was 0.31% (5/1 595). The time interval from the first visit to the first nucleic acid detection of the confirmed monitoring cases and other confirmed cases was statistically insignificant (P>0.05). Conclusions: The monitoring system of COVID-19 based on the health big data platform was working well but the confirmed cases monitoring detection rate need to be improved.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Big Data , China/epidemiology , Cities , Disease Outbreaks , Humans , Pandemics , Population Surveillance , RNA, Viral/genetics , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction
14.
Ocul Immunol Inflamm ; 28(6): 916-921, 2020 Aug 17.
Article in English | MEDLINE | ID: covidwho-737751

ABSTRACT

PURPOSES: To describe the prevalence of ocular features among COVID-19 patients and their relationship with clinical data, inflammatory markers and respiratory support therapy (including CPAP); to investigate SARS-CoV-2 in ocular secretions of symptomatic patients. METHODS: 172 COVID-19 patients were evaluated for presence of ocular manifestations. Clinical and laboratory data were also reviewed. Conjunctival swabs were analyzed for SARS-CoV-2 by RT-PCR. RESULTS: Forty-five patients (26.2%) reported ocular manifestations. Patients treated with CPAP were more likely to have ocular abnormalities (p <.01). The presence of ocular symptoms was not associated with more significant alterations on blood tests. Conjunctival swabs from patients with suspect conjunctivitis yielded negative results for SARS-CoV-2. CONCLUSIONS: Ocular features are not infrequent in COVID-19 patients, but the presence of SARS-CoV-2 in ocular secretions is low. Ocular manifestations in hospitalized COVID-19 patients can also be a consequence of respiratory support therapy. Prevention of possible transmission through ocular secretions is still recommended.


Subject(s)
Betacoronavirus/genetics , Conjunctiva/virology , Conjunctivitis, Viral/etiology , Coronavirus Infections/complications , Pandemics , Pneumonia, Viral/complications , RNA, Viral/analysis , Conjunctivitis, Viral/diagnosis , Conjunctivitis, Viral/virology , Coronavirus Infections/epidemiology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Pneumonia, Viral/epidemiology
15.
Int J Mol Sci ; 21(17)2020 Aug 27.
Article in English | MEDLINE | ID: covidwho-737661

ABSTRACT

A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5' untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or otherwise measured. To this end, we have combined molecular dynamics simulations with previous Nuclear Magnetic Resonance measurements for stem loop 2 of SARS-CoV-1 to refine 3D structure predictions of that stem loop. We find that relatively short sampling times allow for loop rearrangement from predicted structures determined in absence of water or ions, to structures better aligned with experimental data. We then use molecular dynamics to predict the refined structure of the transcription regulatory leader sequence (TRS-L) region which includes stem loop 3, and show that arrangement of the loop around exchangeable monovalent potassium can interpret the conformational equilibrium determined by in-cell dimethyl sulfate (DMS) data.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/virology , Pneumonia, Viral/virology , 5' Untranslated Regions/genetics , Humans , Inverted Repeat Sequences/genetics , Molecular Dynamics Simulation , Nucleic Acid Conformation , Pandemics , RNA, Viral/genetics
16.
J Diabetes Res ; 2020: 1652403, 2020.
Article in English | MEDLINE | ID: covidwho-733124

ABSTRACT

Background: Since December 2019, novel coronavirus- (SARS-CoV-2) infected pneumonia (COVID-19) has rapidly spread throughout China. This study is aimed at describing the characteristics of COVID-19 patients in Wuhan. Methods: 199 COVID-19 patients were admitted to Wuhan Red Cross Hospital in China from January 24th to March 15th. The cases were divided into diabetic and nondiabetic groups according to the history of taking antidiabetic drugs or by plasma fasting blood glucose level at admission, and the difference between groups were compared. Results: Among 199 COVID-19 patients, 76 were diabetic and 123 were nondiabetic. Compared with nondiabetics, patients with diabetes had an older age, high levels of fasting plasma glucose (FPG), D-dimer, white blood cell, blood urea nitrogen (BUN) and total bilirubin (TBIL), lower levels of lymphocyte, albumin and oxygen saturation (SaO2), and higher mortality (P < 0.05). The two groups showed no difference in clinical symptoms. Diabetes, higher level of D-dimer at admission, and lymphocyte count less than 0.6 × 109/L at admission were associated with increasing odds of death. Antidiabetic drugs were associated with decreasing odds of death. Treatment with low molecular weight heparin was not related to odds of death. Conclusion: The mortality rate of COVID-19 patients with diabetes was significantly higher than those without diabetes. Diabetes, higher level of D-dimer, and lymphocyte count less than 0.6 × 109/L at admission were the risk factors associated with in-hospital death.


Subject(s)
Coronavirus Infections/complications , Coronavirus Infections/mortality , Diabetes Complications/mortality , Diabetes Mellitus/mortality , Pneumonia, Viral/complications , Pneumonia, Viral/mortality , Aged , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Case-Control Studies , China/epidemiology , Clinical Laboratory Techniques/methods , Comorbidity , Coronavirus Infections/blood , Coronavirus Infections/diagnosis , Diabetes Complications/blood , Diabetes Complications/drug therapy , Diabetes Complications/epidemiology , Diabetes Mellitus/blood , Diabetes Mellitus/drug therapy , Diabetes Mellitus/epidemiology , Female , Hospital Mortality , Humans , Hypoglycemic Agents/therapeutic use , Length of Stay/statistics & numerical data , Male , Middle Aged , Pandemics , Patient Admission/statistics & numerical data , Pneumonia, Viral/blood , Pneumonia, Viral/diagnosis , RNA, Viral/analysis , Retrospective Studies , Risk Factors
17.
PLoS One ; 15(8): e0238490, 2020.
Article in English | MEDLINE | ID: covidwho-732989

ABSTRACT

SARS-CoV-2 is still rampaging throughout the world while the many evolutionary studies on it are simultaneously springing up. Researchers have simply utilized the public RNA-seq data to find out the so-called SNPs in the virus genome. The evolutionary analyses were largely based on these mutations. Here, we claim that we reliably detected A-to-G RNA modifications in the RNA-seq data of SARS-CoV-2 with high signal to noise ratios, presumably caused by the host's deamination enzymes. Intriguingly, since SARS-CoV-2 is an RNA virus, it is technically impossible to distinguish SNPs and RNA modifications from the RNA-seq data alone without solid evidence, making it difficult to tell the evolutionary patterns behind the mutation spectrum. Researchers should clarify their biological significance before they automatically regard the mutations as SNPs or RNA modifications. This is not a problem for DNA organisms but should be seriously considered when we are investigating the RNA viruses.


Subject(s)
Betacoronavirus/genetics , Evolution, Molecular , Polymorphism, Single Nucleotide , RNA, Viral/genetics , Base Sequence , Coronavirus Infections , Humans , Mutation Rate , Pandemics , Pneumonia, Viral , RNA-Seq
18.
Front Cell Infect Microbiol ; 10: 445, 2020.
Article in English | MEDLINE | ID: covidwho-732914

ABSTRACT

A new type of coronavirus-induced pneumonia eventually termed "coronavirus disease 2019" (COVID-19) was diagnosed in patients in Wuhan (Hubei Province, China) in December 2019, and soon spread worldwide. To improve the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we analyzed the results of viral nucleic acid and serum-specific antibody tests on clinical samples from 20 patients with SARS-CoV-2 infection diagnosed at the First Affiliated Hospital of Guangzhou Medical University in China. By comparing various sample types collected from COVID-19 patients, we revealed multiple pathways for SARS-CoV-2 shedding, and a prolonged detectable period for viral nucleic acid test in sputum specimens, demonstrating that the timeline of the viral shedding is of great value in determining the time of release from quarantine or discharge from hospital. We also recommend for the application of serological test to assist in confirming SARS-CoV-2 infection judged by viral nucleic acid test, especially when COVID-19-related symptoms have appeared and the viral nucleic acid test was negative. Our findings are critical for the diagnosis of SARS-CoV-2 infection and for determining deadline of restriction measures to prevent transmission caused by convalescent patients with COVID-19.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Feces/virology , Immunoglobulin G/blood , Immunoglobulin M/blood , Pneumonia, Viral/diagnosis , Sputum/virology , Antibodies, Viral/blood , Betacoronavirus/genetics , Betacoronavirus/physiology , Female , Humans , Male , Middle Aged , Pandemics , RNA, Viral/analysis , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Serologic Tests , Virus Shedding
19.
Cell Physiol Biochem ; 54(4): 767-790, 2020 Aug 25.
Article in English | MEDLINE | ID: covidwho-729851

ABSTRACT

The pandemic of the severe acute respiratory syndrome coronavirus (SARS-CoV)-2 at the end of 2019 marked the third outbreak of a highly pathogenic coronavirus affecting the human population in the past twenty years. Cross-species zoonotic transmission of SARS-CoV-2 has caused severe pathogenicity and led to more than 655,000 fatalities worldwide until July 28, 2020. Outbursts of this virus underlined the importance of controlling infectious pathogens across international frontiers. Unfortunately, there is currently no clinically approved antiviral drug or vaccine against SARS-CoV-2, although several broad-spectrum antiviral drugs targeting multiple RNA viruses have shown a positive response and improved recovery in patients. In this review, we compile our current knowledge of the emergence, transmission, and pathogenesis of SARS-CoV-2 and explore several features of SARS-CoV-2. We emphasize the current therapeutic approaches used to treat infected patients. We also highlight the results of in vitro and in vivo data from several studies, which have broadened our knowledge of potential drug candidates for the successful treatment of patients infected with and discuss possible virus and host-based treatment options against SARS-CoV-2.


Subject(s)
Betacoronavirus , Coronavirus Infections , Pandemics , Pneumonia, Viral , Animals , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Betacoronavirus/drug effects , Betacoronavirus/genetics , Betacoronavirus/physiology , Coronaviridae/pathogenicity , Coronaviridae Infections/epidemiology , Coronaviridae Infections/virology , Coronavirus Infections/drug therapy , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Coronavirus Infections/therapy , Coronavirus Infections/transmission , Cytokine Release Syndrome/etiology , Cytokine Release Syndrome/prevention & control , Cytokines/antagonists & inhibitors , Drug Delivery Systems , Endocytosis/drug effects , Forecasting , Genome, Viral , Global Health , Humans , Immunity, Herd , Immunization, Passive , Pandemics/prevention & control , Peptide Hydrolases/pharmacology , Peptide Hydrolases/therapeutic use , Pneumonia, Viral/drug therapy , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , RNA, Viral/genetics , Receptors, Virus/antagonists & inhibitors , Receptors, Virus/metabolism , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Spike Glycoprotein, Coronavirus/metabolism , Viral Vaccines , Virus Internalization/drug effects , Virus Replication/drug effects , Zoonoses
20.
J Int Med Res ; 48(8): 300060520949067, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-729470

ABSTRACT

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid test is currently the gold standard for diagnosing coronavirus disease 2019 (COVID-19). This disease requires high-quality viral nucleic acid tests, and selecting the type of specimen from patients, who are at different disease stages, to use in the nucleic acid test is challenging. This article reports in detail the diagnosis and treatment process for two patients with confirmed COVID-19 and analyzes the results of the SARS-CoV-2 nucleic acid tests that were used for different types of specimens (sputum from deep cough, nasopharyngeal swab, and feces). The nucleic acid testing results of sputum from deep cough showed the best performance for positive detection. Our findings provide a reference for selecting the most suitable specimen for the clinical diagnosis of COVID-19 and improving the positive detection rate.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Molecular Diagnostic Techniques/methods , Pneumonia, Viral/diagnosis , Aged , Humans , Male , Middle Aged , Pandemics , RNA, Viral/analysis
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