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2.
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
3.
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
4.
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
5.
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
6.
J Travel Med ; 27(5)2020 08 20.
Article in English | MEDLINE | ID: covidwho-729174

ABSTRACT

BACKGROUND: Wastewater-based epidemiology (WBE) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be an important source of information for coronavirus disease 2019 (COVID-19) management during and after the pandemic. Currently, governments and transportation industries around the world are developing strategies to minimize SARS-CoV-2 transmission associated with resuming activity. This study investigated the possible use of SARS-CoV-2 RNA wastewater surveillance from airline and cruise ship sanitation systems and its potential use as a COVID-19 public health management tool. METHODS: Aircraft and cruise ship wastewater samples (n = 21) were tested for SARS-CoV-2 using two virus concentration methods, adsorption-extraction by electronegative membrane (n = 13) and ultrafiltration by Amicon (n = 8), and five assays using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) and RT-droplet digital PCR (RT-ddPCR). Representative qPCR amplicons from positive samples were sequenced to confirm assay specificity. RESULTS: SARS-CoV-2 RNA was detected in samples from both aircraft and cruise ship wastewater; however concentrations were near the assay limit of detection. The analysis of multiple replicate samples and use of multiple RT-qPCR and/or RT-ddPCR assays increased detection sensitivity and minimized false-negative results. Representative qPCR amplicons were confirmed for the correct PCR product by sequencing. However, differences in sensitivity were observed among molecular assays and concentration methods. CONCLUSIONS: The study indicates that surveillance of wastewater from large transport vessels with their own sanitation systems has potential as a complementary data source to prioritize clinical testing and contact tracing among disembarking passengers. Importantly, sampling methods and molecular assays must be further optimized to maximize detection sensitivity. The potential for false negatives by both wastewater testing and clinical swab testing suggests that the two strategies could be employed together to maximize the probability of detecting SARS-CoV-2 infections amongst passengers.


Subject(s)
Aircraft , Betacoronavirus/isolation & purification , Coronavirus Infections , Pandemics , Pneumonia, Viral , RNA, Viral/isolation & purification , Ships , Waste Water/virology , Humans , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity , Travel
7.
J Infect Dis ; 222(6): 903-909, 2020 08 17.
Article in English | MEDLINE | ID: covidwho-726096

ABSTRACT

High-throughput molecular testing for severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) may be enabled by group testing in which pools of specimens are screened, and individual specimens tested only after a pool tests positive. Several laboratories have recently published examples of pooling strategies applied to SARS-CoV-2 specimens, but overall guidance on efficient pooling strategies is lacking. Therefore we developed a model of the efficiency and accuracy of specimen pooling algorithms based on available data on SAR-CoV-2 viral dynamics. For a fixed number of tests, we estimate that programs using group testing could screen 2-20 times as many specimens compared with individual testing, increase the total number of true positive infections identified, and improve the positive predictive value of results. We compare outcomes that may be expected in different testing situations and provide general recommendations for group testing implementation. A free, publicly-available Web calculator is provided to help inform laboratory decisions on SARS-CoV-2 pooling algorithms.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Specimen Handling/methods , Algorithms , Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Humans , Incidence , Pandemics , Pneumonia, Viral/diagnosis , Predictive Value of Tests , RNA, Viral/genetics , RNA, Viral/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Viral Load/methods
8.
J Immunol Res ; 2020: 8624963, 2020.
Article in English | MEDLINE | ID: covidwho-721226

ABSTRACT

Single-cell RNA sequencing allows highly detailed profiling of cellular immune responses from limited-volume samples, advancing prospects of a new era of systems immunology. The power of single-cell RNA sequencing offers various opportunities to decipher the immune response to infectious diseases and vaccines. Here, we describe the potential uses of single-cell RNA sequencing methods in prophylactic vaccine development, concentrating on infectious diseases including COVID-19. Using examples from several diseases, we review how single-cell RNA sequencing has been used to evaluate the immunological response to different vaccine platforms and regimens. By highlighting published and unpublished single-cell RNA sequencing studies relevant to vaccinology, we discuss some general considerations how the field could be enriched with the widespread adoption of this technology.


Subject(s)
Betacoronavirus/immunology , Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , RNA-Seq/methods , Single-Cell Analysis , Vaccinology/methods , Viral Vaccines/administration & dosage , Animals , Cell Line , Clinical Trials as Topic , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Disease Models, Animal , Drug Evaluation, Preclinical , Host-Pathogen Interactions/genetics , Host-Pathogen Interactions/immunology , Humans , Immunity, Cellular/genetics , Immunity, Innate/genetics , Immunogenicity, Vaccine , Pneumonia, Viral/epidemiology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , RNA, Viral/isolation & purification , Viral Vaccines/immunology
9.
Viruses ; 12(8)2020 08 07.
Article in English | MEDLINE | ID: covidwho-713633

ABSTRACT

Rapid large-scale testing is essential for controlling the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. As a result of the large demand for testing, commercial RNA extraction kits may be limited and, alternatively, non-commercial protocols are needed. Here, we provide a magnetic bead RNA extraction protocol that is predominantly based on in-house made reagents and is performed in 96-well plates supporting large-scale testing. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Importantly, the presented diagnostic workflow can be quickly set up in a laboratory without access to an automated pipetting robot.


Subject(s)
Betacoronavirus/chemistry , Betacoronavirus/genetics , Clinical Laboratory Techniques/methods , Coronavirus Infections/virology , Pneumonia, Viral/virology , RNA, Viral/isolation & purification , Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Humans , Magnetic Phenomena , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , Pandemics , Pneumonia, Viral/diagnosis , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/methods , Reverse Transcription , Sensitivity and Specificity
10.
J Med Microbiol ; 69(8): 1114-1123, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-713623

ABSTRACT

Introduction. Coronavirus disease 2019 (COVID-19) is an infectious disease caused by Severe Acute Respiratory Corona Virus-2 (SARS-CoV-2). The disease was first identified in December 2019 in Wuhan, the capital of China's Hubei province, and has since spread globally, resulting in the ongoing 2019-2020 corona virus pandemic. SARS-CoV-2 is closely related to the original SARS-CoV. It is thought to have a zoonotic origin. The virus is primarily spread between people during close contact, often via small droplets produced by coughing, sneezing or talking. People may also become infected by touching a contaminated surface and then touching their face. COVID-19 patients currently remain the primary source of infection. An epidemiological survey indicated that the general population is susceptible to SARS-CoV-2. The spectrum of this disease ranges from mild to life-threatening. Fever is the most common symptom, although older people and those with comorbidities may experience fever later in the disease. Other common symptoms include cough, loss of appetite, fatigue, shortness of breath, sputum production, and muscle and joint pains. Symptoms such as nausea, vomiting and diarrhea have been observed in varying percentages. Some cases might progress promptly to acute respiratory distress syndrome (ARDS) and/or multiple organ function failure. Asymptomatic carriers and those in the incubation period may also be infectious.Aim. To determine the epidemiological and clinical characteristics of patients presenting with COVID-19 at the screening clinic of a tertiary care hospital in Peshawar, Pakistan.Methodology. In this descriptive study, we analysed data of patients presenting to a newly established Covid-19 screening clinic in Rehman Medical Institute. Anyone who reported with new onset fever and/or cough was tested for SARS-CoV-2 in the screening clinic. We documented and analysed demographic, epidemiological and clinical characteristics, which included age, sex, travel history, clinical features, comorbidities and laboratory data of patients confirmed by real-time reverse-transcription (RT)-PCR at Rehman Medical Institute, Peshawar, Pakistan from 15 March till 21 April 2020. Paired specimens of throat swabs and nasal swabs were obtained from 845 patients, ribonucleic acid (RNA) was extracted and tested for SARS-CoV-2 by the RT-PCR assay.Results. A total of 845 specimens were taken as described above. The positive rate for SARS-CoV-2 was about 14.3%. Male and older population had a significantly higher positive rate. Of the 121 patients infected with SARS-CoV-2, the mean age was 43.19 years (sd, 17.57) and the infections were more frequent among male gender accounting for 85 (70.25 %) patients. Common symptoms included fever (88 patients, 72 %), cough (72 patients, 59.5 %) and shortness of breath (69 patients, 57 %). Twenty-two (18 %) patients had recent travel history outside Pakistan in the previous 14 days, the majority of whom had returned back from Saudi Arabia.Conclusion. In this single-centre, prospective, descriptive study, fever, cough and shortness of breath were the most common symptoms. Old age (>50 years), chronic underlying comorbidities and travel history may be risk factors. Therefore, we concluded that viral nucleic acid amplification tests (NAAT) played an important role in identifying SARS-CoV-2 infection in a screening clinic, which helped with isolation and cohorting of these patients.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Disease Outbreaks , Pneumonia, Viral/epidemiology , Adolescent , Adult , Age Distribution , Aged , Aged, 80 and over , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Child , Child, Preschool , Comorbidity , Coronavirus Infections/diagnosis , DNA, Complementary/genetics , Female , Humans , Infant , Male , Mass Screening , Middle Aged , Pandemics , Pneumonia, Viral/diagnosis , Prospective Studies , RNA, Viral/genetics , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction , Risk Factors , Sex Distribution , Travel , Young Adult
12.
Urol Int ; 104(9-10): 678-683, 2020.
Article in English | MEDLINE | ID: covidwho-709600

ABSTRACT

INTRODUCTION: The presence of new coronavirus (SARS-CoV-2) in semen and the possibility of sexual transmission have become new subjects of curiosity. There is a discrepancy regarding this issue in the literature. The presence of SARS-CoV-2 in semen has been investigated in a limited number of studies, and mostly in recovering patients. We aimed to investigate the presence of SARS-CoV-2 RNA in semen of patients with a positive nasopharyngeal swab test for SARS-CoV-2 in the acute stage. METHODS: We enrolled adult male patients who were hospitalized with confirmed SARS-COV-2 infection in the study. In addition to routine laboratory and radiological tests, semen sample was obtained from volunteers and transferred to the Turkish Public Health Institution, National Virology Laboratory. The samples were processed for the detection of SARS-CoV-2 RNA on the day of collection. RESULTS: Sixteen patients were included in the study. The median age was 33.5 years (18-54). All but one had respiratory symptoms. None of the patients had a history or symptoms of urogenital disease. All semen samples were obtained during hospitalization and in the acute stage of the infection. The median time to obtain a semen sample after positive nasopharyngeal test was 1 day (0-7). All semen samples were detected as negative for SARS-CoV-2 PCR. DISCUSSION/CONCLUSION: Although all semen samples were obtained in acute stage of the infection when the nasopharyngeal swab test was positive, we did not detect SARS-CoV-2 in semen. The results of our study support the thought that sexual transmission via semen does not have an important role in the person-to-person transmission of SARS-CoV-2. We think that our study will provide new information to fill the gap in the literature.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Pneumonia, Viral/virology , RNA, Viral/isolation & purification , Semen/virology , Adolescent , Adult , Betacoronavirus/genetics , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/transmission , Hospitalization , Humans , Male , Middle Aged , Nasopharynx/virology , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/transmission , Prospective Studies , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Time Factors , Young Adult
13.
J Infect Dis ; 222(4): 551-555, 2020 07 23.
Article in English | MEDLINE | ID: covidwho-704462

ABSTRACT

We simulated 3 transmission modes, including close-contact, respiratory droplets and aerosol routes, in the laboratory. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be highly transmitted among naive human angiotensin-converting enzyme 2 (hACE2) mice via close contact because 7 of 13 naive hACE2 mice were SARS-CoV-2 antibody seropositive 14 days after being introduced into the same cage with 3 infected-hACE2 mice. For respiratory droplets, SARS-CoV-2 antibodies from 3 of 10 naive hACE2 mice showed seropositivity 14 days after introduction into the same cage with 3 infected-hACE2 mice, separated by grids. In addition, hACE2 mice cannot be experimentally infected via aerosol inoculation until continued up to 25 minutes with high viral concentrations.


Subject(s)
Betacoronavirus , Coronavirus Infections/transmission , Pneumonia, Viral/transmission , Aerosols , Anal Canal/virology , Animals , Antibodies, Viral/blood , Betacoronavirus/genetics , Betacoronavirus/immunology , Betacoronavirus/isolation & purification , Chlorocebus aethiops , Female , Humans , Immunoglobulin G/blood , Lung/pathology , Lung/virology , Male , Mice , Mice, Transgenic , Pandemics , Peptidyl-Dipeptidase A/genetics , Pharynx/virology , RNA, Viral/isolation & purification , Respiratory System/virology , Risk , Specific Pathogen-Free Organisms , Time Factors , Vero Cells , Viral Load , Weight Loss
14.
15.
Braz J Microbiol ; 51(3): 1117-1123, 2020 Sep.
Article in English | MEDLINE | ID: covidwho-695574

ABSTRACT

In March 2020, WHO declared a pandemic state due to SARS-CoV-2 having spread. TaqMan-based real-time RT-qPCR is currently the gold standard for COVID-19 diagnosis. However, it is a high-cost assay, inaccessible for the majority of laboratories around the world, making it difficult to diagnose on a large scale. The objective of this study was to standardize lower cost molecular methods for SARS-CoV-2 identification. E gene primers previously determined for TaqMan assays by Colman et al. (2020) were adapted in SYBR Green assay and RT-PCR conventional. The cross-reactivity test was performed with 17 positive samples for other respiratory viruses, and the sensibility test was performed with 8 dilutions (10 based) of SARS-CoV-2 isolated and 63 SARS-CoV-2-positive samples. The SYBR Green assays and conventional RT-PCR have not shown amplification of the 17 respiratory samples positives for other viruses. The SYBR Green-based assay was able to detect all 8 dilutions of the isolate. The conventional PCR detected until 107 dilution, both assays detected the majority of the 63 samples, 98.42% of positivity in SYBR Green, and 93% in conventional PCR. The average Ct variation between SYBR Green and TaqMan was 1.92 and the highest Ct detected by conventional PCR was 35.98. Both of the proposed assays are less sensitive than the current gold standard; however, our data shows a low sensibility variation, suggesting that these methods could be used by laboratories as a lower cost molecular method for SARS-CoV-2 diagnosis.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/diagnosis , Fluorescent Dyes/economics , Organic Chemicals/economics , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction/economics , Adolescent , Adult , Animals , Betacoronavirus/genetics , Child , Chlorocebus aethiops , Coronavirus Infections/economics , Cross Reactions , Humans , Middle Aged , Nasopharynx/virology , Oropharynx/virology , Pandemics/economics , Pneumonia, Viral/economics , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction/methods , Sensitivity and Specificity , Vero Cells , Young Adult
16.
J Infect Dis ; 222(6): 910-918, 2020 08 17.
Article in English | MEDLINE | ID: covidwho-694657

ABSTRACT

BACKGROUND: Despite the ongoing spread of coronavirus disease 2019 (COVID-19), knowledge about factors affecting prolonged viral excretion is limited. METHODS: In this study, we retrospectively collected data from 99 hospitalized patients with coronavirus disease 2019 (COVID-19) between 19 January and 17 February 2020 in Zhejiang Province, China. We classified them into 2 groups based on whether the virus test results eventually became negative. Cox proportional hazards regression was used to evaluate factors associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding. RESULTS: Among 99 patients, 61 patients had SARS-CoV-2 clearance (virus-negative group), but 38 patients had sustained positive results (virus-positive group). The median duration of SARS-CoV-2 excretion was 15 (interquartile range, 12-19) days among the virus-negative patients. The shedding time was significantly increased if the fecal SARS-CoV-2 RNA test result was positive. Male sex (hazard ratio [HR], 0.58 [95% confidence interval {CI}, .35-.98]), immunoglobulin use (HR, 0.42 [95% CI, .24-.76]), APACHE II score (HR, 0.89 [95% CI, .84-.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. Antiviral therapy and corticosteroid treatment were not independent factors. CONCLUSIONS: SARS-CoV-2 RNA clearance time was associated with sex, disease severity, and lymphocyte function. The current antiviral protocol and low-to-moderate dosage of corticosteroid had little effect on the duration of viral excretion.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Pneumonia, Viral/virology , Virus Shedding , Adrenal Cortex Hormones/therapeutic use , Adult , Antiviral Agents/therapeutic use , China , Coronavirus Infections/drug therapy , Coronavirus Infections/epidemiology , Feces/virology , Female , Humans , Lymphocytes , Male , Middle Aged , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/epidemiology , Proportional Hazards Models , RNA, Viral/isolation & purification , Retrospective Studies , Risk Factors , Severity of Illness Index , Sex Factors , Time Factors
18.
Sci Rep ; 10(1): 12732, 2020 07 29.
Article in English | MEDLINE | ID: covidwho-691060

ABSTRACT

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China in late 2019, and its resulting coronavirus disease, COVID-19, was declared a pandemic by the World Health Organization on March 11, 2020. The rapid global spread of COVID-19 represents perhaps the most significant public health emergency in a century. As the pandemic progressed, a continued paucity of evidence on routes of SARS-CoV-2 transmission has resulted in shifting infection prevention and control guidelines between classically-defined airborne and droplet precautions. During the initial isolation of 13 individuals with COVID-19 at the University of Nebraska Medical Center, we collected air and surface samples to examine viral shedding from isolated individuals. We detected viral contamination among all samples, supporting the use of airborne isolation precautions when caring for COVID-19 patients.


Subject(s)
Aerosols/analysis , Betacoronavirus/genetics , Coronavirus Infections/pathology , Pneumonia, Viral/pathology , Air Pollutants/analysis , Betacoronavirus/isolation & purification , Betacoronavirus/physiology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Humans , Infection Control/methods , Pandemics , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Public Health , RNA, Viral/isolation & purification , RNA, Viral/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Time Factors
19.
Am J Nephrol ; 51(8): 669-674, 2020.
Article in English | MEDLINE | ID: covidwho-691050

ABSTRACT

BACKGROUND: The COVID-19 pandemic has affected the end-stage kidney disease (ESKD) population, with high mortality rates reported among patients on hemodialysis. However, the degree to which it has affected the peritoneal dialysis (PD) population in the United States has not yet been elucidated. In this report, we describe the clinical characteristics, presentations, clinical course, and outcomes of ESKD patients on PD hospitalized with COVID-19. METHODS: We describe the characteristics, presentation, and outcomes of adult ESKD patients on chronic PD hospitalized with CO-VID-19 in our 13 major hospitals in the NY health system using descriptive statistical analysis. RESULTS: Of 419 hospitalized patients with ESKD, 11 were on chronic PD therapy (2.6%). Among those 11, 3 patients required mechanical ventilation, 2 of whom died. Of the entire cohort, 9 of the 11 patients (82%) were discharged alive. While fever was a common presentation, more than half of our patients also presented with diarrhea. Interestingly, 3 patients were diagnosed with culture-negative peritonitis during their hospitalization. Seven patients reported positive SARS-CoV-2 exposure from a member of their household. CONCLUSION: Hospitalized patients on PD with COVID-19 had a relatively mild course, and majority of them were discharged home.


Subject(s)
Betacoronavirus/isolation & purification , Coronavirus Infections/epidemiology , Kidney Failure, Chronic/therapy , Peritoneal Dialysis/adverse effects , Peritonitis/epidemiology , Pneumonia, Viral/epidemiology , Adult , Aged , Betacoronavirus/genetics , Coronavirus Infections/complications , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Electronic Health Records/statistics & numerical data , Female , Hospital Mortality , Hospitalization/statistics & numerical data , Humans , Kidney Failure, Chronic/complications , Kidney Failure, Chronic/mortality , Male , Middle Aged , New York/epidemiology , Pandemics , Peritonitis/diagnosis , Pneumonia, Viral/complications , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , RNA, Viral/isolation & purification
20.
Virulence ; 11(1): 964-967, 2020 12.
Article in English | MEDLINE | ID: covidwho-690823

ABSTRACT

Currently, testing for coronavirus is performed with time and personnel consuming PCR assays. The aim of this study was to evaluate the sensitivity, specificity and capacity of a fully automated, random access high-throughput real-time PCR-based diagnostic platform for the detection of SARS-CoV-2. The NeuMoDx N96 system displayed an equal or better detection rate for SARS-CoV-2 compared with the LightCycler 480II system and showed a specificity of 100%. The median PCR run time for all 28 PCR runs was 91 (IQR 84-97) minutes. The capacity of the NeuMoDx N96 could easily surpass the capacity of most currently used molecular test systems and significantly reduce the turn-around time.


Subject(s)
Betacoronavirus/isolation & purification , High-Throughput Nucleotide Sequencing/methods , RNA, Viral/isolation & purification , Real-Time Polymerase Chain Reaction/methods , Betacoronavirus/genetics , High-Throughput Nucleotide Sequencing/instrumentation , High-Throughput Nucleotide Sequencing/standards , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/instrumentation , Real-Time Polymerase Chain Reaction/standards , Reproducibility of Results , Sensitivity and Specificity , Time Factors
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