Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 177
Filter
2.
Sci Rep ; 12(1): 3706, 2022 03 08.
Article in English | MEDLINE | ID: covidwho-1908236

ABSTRACT

Scaling up SARS-CoV-2 testing and tracing continues to be plagued with the limitation of the sample collection method, which requires trained healthcare workers to perform and causes discomfort to the patients. In response, we assessed the performance and user preference of gargle specimens for qRT-PCR-based detection of SARS-CoV-2 in Indonesia. Inpatients who had recently been diagnosed with COVID-19 and outpatients who were about to perform qRT-PCR testing were asked to provide nasopharyngeal and oropharyngeal (NPOP) swabs and self-collected gargle specimens. We demonstrated that self-collected gargle specimens can be an alternative specimen to detect SARS-CoV-2 and the viral RNA remained stable for 31 days at room temperature storage. The developed method was validated for use on multiple RNA extraction kits and commercially available COVID-19 RT-PCR kits. Our developed method achieved a sensitivity of 91.38% when compared to paired NPOP swab specimens (Ct < 35), with 97.10% of patients preferring the self-collected gargle method.


Subject(s)
COVID-19/diagnosis , Saliva/virology , Specimen Handling/methods , COVID-19/virology , Humans , Mouthwashes/chemistry , Nasopharynx/virology , Oropharynx/virology , RNA, Viral/analysis , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
3.
J Dent ; 123: 104203, 2022 08.
Article in English | MEDLINE | ID: covidwho-1895174

ABSTRACT

OBJECTIVE: Using a battery of preclinical tests to support development of a light-based treatment for COVID-19, establish a range of 425 nm light doses that are non-hazardous to the tissues of the oral cavity and assess whether a 425 nm light dose in this non-hazardous range can inactivate SARS-CoV-2 in artificial saliva. METHODS: The potential hazards to oral tissues associated with a range of acute 425 nm light doses were assessed using a battery of four preclinical tests: (1) cytotoxicity, using well-differentiated human large airway and buccal epithelial models; (2) toxicity to commensal oral bacteria, using a panel of model organisms; (3) light-induced histopathological changes, using ex vivo porcine esophageal tissue, and (4) thermal damage, by dosing the oropharynx of intact porcine head specimens. Then, 425 nm light doses established as non-hazardous using these tests were evaluated for their potential to inactivate SARS-CoV-2 in artificial saliva. RESULTS: A dose range was established at which 425 nm light is not cytotoxic in well-differentiated human large airway or buccal epithelial models, is not cytotoxic to a panel of commensal oral bacteria, does not induce histopathological damage in ex vivo porcine esophageal tissue, and does not induce thermal damage to the oropharynx of intact porcine head specimens. Using these tests, no hazards were observed for 425 nm light doses less than 63 J/cm2 delivered at irradiance less than 200 mW/cm2. A non-hazardous 425 nm light dose in this range (30 J/cm2 at 50 mW/cm2) was shown to inactivate SARS-CoV-2 in vitro in artificial saliva. CONCLUSION: Preclinical hazard assessments and SARS-CoV-2 inactivation efficacy testing were combined to guide the development of a 425 nm light-based treatment for COVID-19. CLINICAL SIGNIFICANCE: The process used here to evaluate the potential hazards associated with 425 nm acute light dosing of the oral cavity to treat COVID-19 can be extended to other wavelengths, anatomical targets, and therapeutic applications to accelerate the development of novel photomedicine treatments.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Humans , Mouth , Oropharynx , Saliva , Saliva, Artificial , Swine
4.
Lancet Infect Dis ; 22(4): 552-561, 2022 04.
Article in English | MEDLINE | ID: covidwho-1839427

ABSTRACT

BACKGROUND: Pharyngeal Chlamydia trachomatis in women might contribute to autoinoculation and transmission to sexual partners. Data for effectiveness of different testing practices for pharyngeal C trachomatis are scarce. We therefore aimed to assess the prevalence of pharyngeal C trachomatis, determinants, and effectiveness of different testing practices in women. METHODS: We did a retrospective cohort study, in which surveillance data for all women visiting sexually transmitted infection clinics in all regions in the Netherlands between Jan 1, 2008, and Dec 31, 2017, were used. We collected consultation-level data and individual-level data from 2016 onwards for sociodemographic characteristics, sexual behaviour in the past 6 months, self-reported symptoms, and STI diagnoses. The primary outcome was the positivity rate of pharyngeal C trachomatis infection compared between routine universal testing (>85% tested pharyngeally per clinic year), selective testing (5-85% tested pharyngeally per clinic year), and incidental testing (<5% pharyngeally tested per clinic year). We calculated the number of missed infections by extrapolating the positivity rate assessed by routine universal testing to all selectively tested women. We used multivariable generalised estimating equations logistic regression analyses to assess independent risk factors for pharyngeal C trachomatis and used the assessed risk factors as testing indicators for comparing alternative testing scenarios. FINDINGS: Between Jan 1, 2008, and Dec 31, 2017, a total of 550 615 consultations with at least one C trachomatis test was recorded, of which 541 945 (98·4%) consultations (including repeat visits) were included in this analysis. Pharyngeal C trachomatis positivity was lower in the routine universal testing group than in the selective testing group (1081 [2·4%; 95% CI 2·2-2·5] of 45 774 vs 3473 [2·9%; 2·8-3·0] of 121 262; p<0·0001). The positivity rate was also higher among consultations done in the incidental testing group (44 [4·1%; 95% CI 3·1-5·5] of 1073; p<0·0001) than in the routine universal testing group. Based on extrapolation, selective testing would have hypothetically missed 64·4% (95% CI 63·5-65·3; 6363 of 9879) of the estimated total of C trachomatis infections. The proportion of pharyngeal-only C trachomatis was comparable between routinely universally tested women (22·9%) and selectively tested women (20·4%), resulting in a difference of 2·5% (95% CI -0·3 to 5·3; p=0·07). When using risk factors for pharyngeal C trachomatis as testing indicators, 15 484 (79·6%) of 19 459 women would be tested to detect 398 (80·6%) of 494 infections. INTERPRETATION: No optimal testing scenario was available for pharyngeal C trachomatis, in which only a selection of high-risk women needs to be tested to find most pharyngeal C trachomatis infections. The relative low prevalence of pharyngeal-only C trachomatis (0·5%) and probably limited clinical and public health effect do not provide support for routine universal testing. FUNDING: Public Health Service South Limburg.


Subject(s)
Chlamydia Infections , Chlamydia trachomatis , Chlamydia Infections/diagnosis , Chlamydia Infections/epidemiology , Female , Humans , Male , Netherlands/epidemiology , Oropharynx , Prevalence , Retrospective Studies
5.
Front Cell Infect Microbiol ; 12: 824578, 2022.
Article in English | MEDLINE | ID: covidwho-1775646

ABSTRACT

Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.


Subject(s)
COVID-19 , Microbiota , Humans , Oropharynx/microbiology , RNA, Ribosomal, 16S/genetics , SARS-CoV-2
6.
Microbiol Spectr ; 10(1): e0059121, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1691413

ABSTRACT

Coronavirus disease 2019 (COVID-19) is a mild to severe respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnostic accuracy of the Centers for Disease Control and Prevention (CDC)- or World Health Organization (WHO)-recommended real-time PCR (RT-qPCR) primers in clinical practice remains unproven. We conducted a prospective study on the accuracy of RT-qPCR using an in-house-designed primer set (iNP) targeting the nucleocapsid protein as well as various recommended and commercial primers. The accuracy was assessed by culturing or seroconversion. We enrolled 12 confirmed COVID-19 patients with a total of 590 clinical samples. When a cutoff value of the cycle threshold (Ct) was set to 35, RT-qPCRs with WHO RdRp primers and CDC N1, N2, and N3 primers showed sensitivity of 42.1% to 63.2% and specificity of 90.5% to 100% in sputum, and sensitivity of 65.2% to 69.6% and specificity of 65.2% to 69.6% in nasopharyngeal samples. The sensitivity and specificity of iNP RT-qPCR in sputum and nasopharyngeal samples were 94.8%/100% and 69.6%/100%, respectively. Sputum testing had the highest sensitivity, followed by nasopharyngeal testing (P = 0.0193); self-collected saliva samples yielded better characteristics than oropharyngeal samples (P = 0.0032). Our results suggest that iNP RT-qPCR has better sensitivity and specificity than RT-PCR with WHO (P < 0.0001) or CDC (N1: P = 0.0012, N2: P = 0.0013, N3: P = 0.0012) primers. Sputum RT-qPCR analysis has the highest sensitivity, followed by nasopharyngeal, saliva, and oropharyngeal assays. Our study suggests that considerable improvement is needed for the RT-qPCR WHO and CDC primer sets for detecting SARS-CoV-2. IMPORTANCE Numerous research campaigns have addressed the vast majority of clinical and diagnostic specificity and sensitivity of various primer sets of SARS-CoV2 viral detection. Despite the impressive progress made to resolve the pandemic, there is still a need for continuous and active improvement of primers used for diagnosis in clinical practice. Our study significantly exceeds the scale of previously published research on the specificity and sensitivity of different primers comparing with different specimens and is the most comprehensive to date in terms of constant monitoring of primer sets of current usage. Henceforth, our results suggest that sputum samples sensitivity is the highest, followed by nasopharyngeal, saliva, and oropharyngeal samples. The CDC recommends the use of oropharyngeal specimens, leading to certain discrepancy between the guidelines set forth by the CDC and IDSA. We proved that the oropharyngeal samples demonstrated the lowest sensitivity for the detection of SARS-CoV-2.


Subject(s)
COVID-19/diagnosis , Real-Time Polymerase Chain Reaction/standards , SARS-CoV-2/isolation & purification , Adult , Aged , COVID-19/virology , Cross Reactions , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Oropharynx/virology , SARS-CoV-2/genetics , Saliva/virology , Sensitivity and Specificity , Sputum/virology , Viral Load , Young Adult
7.
PLoS One ; 17(2): e0263341, 2022.
Article in English | MEDLINE | ID: covidwho-1690730

ABSTRACT

Rapid and accurate detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the successful control of the current global COVID-19 pandemic. The real-time reverse transcription polymerase chain reaction (Real-time RT-PCR) is the most widely used detection technique. This research describes the development of two novel multiplex real-time RT-PCR kits, AccuPower® COVID-19 Multiplex Real-Time RT-PCR Kit (NCVM) specifically designed for use with the ExiStation™48 system (comprised of ExiPrep™48 Dx and Exicycler™96 by BIONEER, Korea) for sample RNA extraction and PCR detection, and AccuPower® SARS-CoV-2 Multiplex Real-Time RT-PCR Kit (SCVM) designed to be compatible with manufacturers' on-market PCR instruments. The limit of detection (LoD) of NCVM was 120 copies/mL and the LoD of the SCVM was 2 copies/µL for both the Pan-sarbecovirus gene and the SARS-CoV-2 gene. The AccuPower® kits demonstrated high precision with no cross reactivity to other respiratory-related microorganisms. The clinical performance of AccuPower® kits was evaluated using the following clinical samples: sputum and nasopharyngeal/oropharyngeal swab (NPS/OPS) samples. Overall agreement of the AccuPower® kits with a Food and Drug Administration (FDA) approved emergency use authorized commercial kit (STANDARD™ M nCoV Real-Time Detection kit, SD BIOSENSOR, Korea) was above 95% (Cohen's kappa coefficient ≥ 0.95), with a sensitivity of over 95%. The NPS/OPS specimen pooling experiment was conducted to verify the usability of AccuPower® kits on pooled samples and the results showed greater than 90% agreement with individual NPS/OPS samples. The clinical performance of AccuPower® kits with saliva samples was also compared with NPS/OPS samples and demonstrated over 95% agreement (Cohen's kappa coefficient > 0.95). This study shows the BIONEER NCVM and SCVM assays are comparable with the current standard confirmation assay and are suitable for effective clinical management and control of SARS-CoV-2.


Subject(s)
COVID-19/virology , Multiplex Polymerase Chain Reaction , Nasopharynx/virology , Oropharynx/virology , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Saliva/virology , Sputum/virology , Cross Reactions , Humans , Limit of Detection , Sensitivity and Specificity
8.
Virus Res ; 310: 198673, 2022 03.
Article in English | MEDLINE | ID: covidwho-1635564

ABSTRACT

This study aimed to investigate the prevalence of COVID-19 in domestic cats, focusing on the disease in the northwest of Iran and then showing the natural transmission of SARS-COV-2 circulating between domestic cats and humans. After receiving ethic codes from Tehran University of Medical Sciences (IR.TUMS.VCR.REC.1399.303) and confirmed by the Center of Communicable Diseases Control (CDC) of Iran, 124 domestic cats were collected from the homes and only one hospital of Meshkin -Shahr district from northwestern Iran where SARS-CoV-2 patients were hospitalized and quarantined during 2020. Samples were prepared from fluid materials of oropharynx and nasopharynx. All samples were tested by real-time PCR (RT-PCR) using specific genes N and ORF1ab in Pasteur Institute of Iran, and then partial sequence analyses of S gene were performed. All collected cats were kept in separated cages until SARS-COV-2 infection was confirmed with the RT-PCR. RT- PCR Ct values of 123 collected cats were ≥40; thus, all of them showed negative results, but one of the collected cats with close contact with its owner, whom confirmed SARS-CoV-2 showed positive results with gene N(Ct=30) and gene ORF1ab (Ct=32). Furthermore, the positive pet cat showed respiratory and gastro-intestinal clinical manifestations, and its owner was infected with SARS-CoV-2 two weeks ago. Cats are susceptible animals to SARS-CoV-2 infection. Epidemiological evidence showed that SARS-COV-2 is able to transmit to healthy cats due to having close contact with its owner as a reverse zoonosis.


Subject(s)
COVID-19 , Cats , SARS-CoV-2 , Animals , COVID-19/epidemiology , COVID-19/veterinary , Cats/virology , Humans , Iran/epidemiology , Nasopharynx/virology , Oropharynx/virology , Pets/virology , Real-Time Polymerase Chain Reaction , SARS-CoV-2/isolation & purification
9.
Forensic Sci Int ; 331: 111168, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1616494

ABSTRACT

Rapid and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in dead bodies is essential to prevent infection among those working with dead bodies. This study focused on the Smart Amplification (SmartAmp) method, which has a short examination time (approximately an hour), is simple to perform, and demonstrates high specificity and sensitivity. This method has already been used for clinical specimens; however, its effectiveness in dead bodies has not been reported. This study examined the SmartAmp method using 11 autopsies or postmortem needle biopsies performed from January to May, 2021 (of these, five cases tested positive for SARS-CoV-2 by quantitative real-time polymerase chain reaction (qRT-PCR) and six cases tested negative). Swab samples were collected from the nasopharynx, oropharynx, or anus and the SmartAmp and qRT-PCR results were compared. For the nasopharynx and oropharynx samples, the same results were obtained for both methods in all cases; however, for the anal swabs, there was one case that was positive according to qRT-PCR but negative according to the SmartAmp method. The SmartAmp method may therefore be less sensitive than qRT-PCR and results may differ in specimens with a low viral load, such as anal swabs. However, in the nasopharynx and oropharynx specimens, which are normally used for testing, the results were the same using each method, suggesting that the SmartAmp method is useful in dead bodies. In the future, the SmartAmp method may be applied not only during autopsies, but also in various situations where dead bodies are handled.


Subject(s)
Cadaver , SARS-CoV-2 , Anal Canal/virology , COVID-19 , COVID-19 Nucleic Acid Testing , Humans , Nasopharynx/virology , Oropharynx/virology , RNA, Viral , SARS-CoV-2/isolation & purification
10.
Diagn Microbiol Infect Dis ; 102(2): 115591, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1596631

ABSTRACT

Testing for SARS-CoV-2 in resource-poor settings remains a considerable challenge. Gold standard nucleic acid tests are expensive and depend on availability of expensive equipment and highly trained laboratory staff. More affordable and easier rapid antigen tests are an attractive alternative. This study assessed field performance of such a test in western Kenya. We conducted a prospective multi-facility field evaluation study of NowCheck COVID-19 Ag-RDT compared to gold standard PCR. Two pairs of oropharyngeal and nasopharyngeal swabs were collected for comparative analysis. With 997 enrolled participants the Ag-RDT had a sensitivity 71.5% (63.2-78.6) and specificity of 97.5% (96.2-98.5) at cycle threshold value <40. Highest sensitivity of 87.7% (77.2-94.5) was observed in samples with cycle threshold values ≤30. NowCheck COVID-19 Ag-RDT performed well at multiple healthcare facilities in an African field setting. Operational specificity and sensitivity were close to WHO-recommended thresholds.


Subject(s)
Antigens, Viral/analysis , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Nasopharynx/virology , Oropharynx/virology , SARS-CoV-2/immunology , Adult , Child , Cross-Sectional Studies , Developing Countries , Diagnostic Tests, Routine , Female , Humans , Kenya , Male , Middle Aged , Point-of-Care Testing , Prospective Studies , Sensitivity and Specificity
11.
Med Princ Pract ; 31(1): 93-97, 2022.
Article in English | MEDLINE | ID: covidwho-1562353

ABSTRACT

OBJECTIVES: We aimed to describe the clinical characteristics of SARS-CoV-2 infection and estimate viral shedding duration in respiratory specimens. METHODS: A retrospective cohort study was performed from February 25 to March 25, 2020. In Kuwait, all suspected coronavirus disease 2019 (COVID-19) cases, contacts of cases, and returning travelers were systematically tested for SARS-CoV-2 by RT-PCR. All infected persons, regardless of symptoms, were hospitalized and serially tested until they had two negative results. Descriptive statistics and regression analyses were performed. RESULTS: Two hundred seven cases of SARS-CoV-2 infection were included in this study. About half of the cases were asymptomatic and 1.9% died. The median time to negative RT-PCR was 22 days. Increasing age, ARDS, and low peripheral white blood cell count were associated with prolonged PCR positivity. CONCLUSION: Predictors for prolonged RT-PCR positivity included increasing age, ARDS, and low white blood cell count. The findings of this study may aid in better understanding of the epidemiology of SARS-CoV-2 infection and molecular testing dynamics.


Subject(s)
COVID-19 , Nasopharynx/virology , Oropharynx/virology , SARS-CoV-2 , Virus Shedding , Adult , COVID-19/epidemiology , COVID-19 Nucleic Acid Testing , Female , Hospitalization , Humans , Kuwait/epidemiology , Male , Middle Aged , Respiratory Distress Syndrome , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
12.
Lab Med ; 52(6): e154-e158, 2021 Nov 02.
Article in English | MEDLINE | ID: covidwho-1559980

ABSTRACT

OBJECTIVE: This study aims to evaluate the performance of an antigen-based rapid diagnostic test (RDT) for the detection of the SARS-CoV-2 virus. METHODS: A cross-sectional study was conducted on 677 patients. Two nasopharyngeal swabs and 1 oropharyngeal swab were collected from patients. The RDT was performed onsite by a commercially available immune-chromatographic assay on the nasopharyngeal swab. The nasopharyngeal and oropharyngeal swabs were examined for SARS-CoV-2 RNA by real-time reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay. RESULTS: The overall sensitivity of the SARS-CoV-2 RDT was 34.5% and the specificity was 99.8%. The positive predictive value and negative predictive value of the test were 96.6% and 91.5%, respectively. The detection rate of RDT in RT-qPCR positive results was high (45%) for cycle threshold values <25. CONCLUSION: The utility of RDT is in diagnosing symptomatic patients and may not be particularly suited as a screening tool for patients with low viral load. The low sensitivity of RDT does not qualify its use as a single test in patients who test negative; RT-qPCR continues to be the gold standard test.


Subject(s)
Antigens, Viral/genetics , COVID-19 Serological Testing/standards , COVID-19/diagnosis , Chromatography, Affinity/methods , RNA, Viral/genetics , SARS-CoV-2/genetics , Adolescent , Aged , Aged, 80 and over , Automation, Laboratory , COVID-19/immunology , COVID-19/virology , COVID-19 Serological Testing/methods , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Oropharynx/virology , Reagent Kits, Diagnostic , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/immunology , Sensitivity and Specificity , Viral Load/genetics
13.
J Med Virol ; 93(12): 6837-6840, 2021 12.
Article in English | MEDLINE | ID: covidwho-1544319

ABSTRACT

BACKGROUND: Gargle samples have been proposed as a noninvasive method for detection of SARS-CoV-2 RNA. The clinical performance of gargle specimens diluted in Cobas® PCR Media and in Cobas® Omni Lysis Reagent was compared to oropharyngeal/nasopharyngeal swab (ONPS) for the detection of SARS-CoV-2 RNA. STUDY DESIGN: Participants were recruited prospectively in two COVID-19 screening clinics. In addition to the ONPS, participants gargled with 5 ml of natural spring water split in the laboratory as follows: 1 ml was added to 4.3 ml of polymerase chain reaction (PCR) media and 400 µl was added to 200 µl of lysis buffer. Testing was performed with the Cobas® SARS-CoV-2 test on the Cobas® 6800 or 8800 platforms. RESULTS: Overall, 134/647 (20.7%) participants were considered infected because the ONPS or at least one gargle test was positive. ONPS had, respectively, a sensitivity of 96.3% (95% confidence interval [CI]: 91.3-98.5); both gargle processing methods were slightly less but equally sensitive (90.3% [95% CI: 83.9-94.3]). When ONPS and gargle specimens were both positive, the mean cycle threshold (Ct ) was significantly higher for gargles, suggesting lower viral loads. CONCLUSION: Gargle specimens directly added in PCR Media provide a similar clinical sensitivity to chemical lysis, both having a slightly, not significantly, lower sensitivity to ONPS.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , COVID-19/virology , Nasopharynx/virology , Oropharynx/virology , SARS-CoV-2/genetics , Diagnostic Tests, Routine/methods , Humans , Mass Screening/methods , Prospective Studies , RNA, Viral/genetics , Saliva/virology , Specimen Handling/methods , Viral Load/genetics
14.
Ann Intern Med ; 174(9): 1261-1269, 2021 09.
Article in English | MEDLINE | ID: covidwho-1547664

ABSTRACT

BACKGROUND: New treatment modalities are urgently needed for patients with COVID-19. The World Health Organization (WHO) Solidarity trial showed no effect of remdesivir or hydroxychloroquine (HCQ) on mortality, but the antiviral effects of these drugs are not known. OBJECTIVE: To evaluate the effects of remdesivir and HCQ on all-cause, in-hospital mortality; the degree of respiratory failure and inflammation; and viral clearance in the oropharynx. DESIGN: NOR-Solidarity is an independent, add-on, randomized controlled trial to the WHO Solidarity trial that included biobanking and 3 months of clinical follow-up (ClinicalTrials.gov: NCT04321616). SETTING: 23 hospitals in Norway. PATIENTS: Eligible patients were adults hospitalized with confirmed SARS-CoV-2 infection. INTERVENTION: Between 28 March and 4 October 2020, a total of 185 patients were randomly assigned and 181 were included in the full analysis set. Patients received remdesivir (n = 42), HCQ (n = 52), or standard of care (SoC) (n = 87). MEASUREMENTS: In addition to the primary end point of WHO Solidarity, study-specific outcomes were viral clearance in oropharyngeal specimens, the degree of respiratory failure, and inflammatory variables. RESULTS: No significant differences were seen between treatment groups in mortality during hospitalization. There was a marked decrease in SARS-CoV-2 load in the oropharynx during the first week overall, with similar decreases and 10-day viral loads among the remdesivir, HCQ, and SoC groups. Remdesivir and HCQ did not affect the degree of respiratory failure or inflammatory variables in plasma or serum. The lack of antiviral effect was not associated with symptom duration, level of viral load, degree of inflammation, or presence of antibodies against SARS-CoV-2 at hospital admittance. LIMITATION: The trial had no placebo group. CONCLUSION: Neither remdesivir nor HCQ affected viral clearance in hospitalized patients with COVID-19. PRIMARY FUNDING SOURCE: National Clinical Therapy Research in the Specialist Health Services, Norway.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19/virology , Hydroxychloroquine/therapeutic use , Viral Load/drug effects , Adenosine Monophosphate/therapeutic use , Alanine/therapeutic use , Antibodies, Viral/blood , Biomarkers/blood , COVID-19/complications , COVID-19/mortality , Cause of Death , Female , Hospital Mortality , Humans , Inflammation/virology , Male , Middle Aged , Norway/epidemiology , Oropharynx/virology , Respiratory Insufficiency/virology , SARS-CoV-2/immunology , Severity of Illness Index , Standard of Care , Treatment Outcome
15.
J Infect Dis ; 224(11): 1830-1838, 2021 12 01.
Article in English | MEDLINE | ID: covidwho-1545972

ABSTRACT

BACKGROUND: Elucidating the relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and clinical outcomes is critical for understanding coronavirus disease 2019 (COVID-19). METHODS: The SARS-CoV-2 levels were analyzed by quantitative real-time polymerase chain reaction (RT-qPCR) of nasopharyngeal or oropharyngeal swab specimens collected at baseline, and clinical outcomes were recorded over 60 days from 1362 COVID-19 hospitalized patients enrolled in a multicenter, randomized, placebo-controlled phase 2/3 trial of sarilumab for COVID-19 (ClinicalTrials.gov NCT04315298). RESULTS: In post hoc analyses, higher baseline viral load, measured by both RT-qPCR cycle threshold and log10 copies/mL, was associated with greater supplemental oxygenation requirements and disease severity at study entry. Higher baseline viral load was associated with higher mortality, lower likelihood of improvement in clinical status and supplemental oxygenation requirements, and lower rates of hospital discharge. Viral load was not impacted by sarilumab treatment over time versus placebo. CONCLUSIONS: These data support viral load as an important determinant of clinical outcomes in hospitalized patients with COVID-19 requiring supplemental oxygen or assisted ventilation.


Subject(s)
COVID-19 , Viral Load , COVID-19/diagnosis , COVID-19/mortality , Humans , Nasopharynx/virology , Oropharynx/virology , Respiration, Artificial , SARS-CoV-2
16.
Epidemiol Infect ; 149: e226, 2021 10 26.
Article in English | MEDLINE | ID: covidwho-1537267

ABSTRACT

The corona virus disease-2019 (COVID-19) pandemic began in Wuhan, China, and quickly spread around the world. The pandemic overlapped with two consecutive influenza seasons (2019/2020 and 2020/2021). This provided the opportunity to study community circulation of influenza viruses and severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) in outpatients with acute respiratory infections during these two seasons within the Bavarian Influenza Sentinel (BIS) in Bavaria, Germany. From September to March, oropharyngeal swabs collected at BIS were analysed for influenza viruses and SARS-CoV-2 by real-time polymerase chain reaction. In BIS 2019/2020, 1376 swabs were tested for influenza viruses. The average positive rate was 37.6%, with a maximum of over 60% (in January). The predominant influenza viruses were Influenza A(H1N1)pdm09 (n = 202), Influenza A(H3N2) (n = 144) and Influenza B Victoria lineage (n = 129). In all, 610 of these BIS swabs contained sufficient material to retrospectively test for SARS-CoV-2. SARS-CoV-2 RNA was not detectable in any of these swabs. In BIS 2020/2021, 470 swabs were tested for influenza viruses and 457 for SARS-CoV-2. Only three swabs (0.6%) were positive for Influenza, while SARS-CoV-2 was found in 30 swabs (6.6%). We showed that no circulation of SARS-CoV-2 was detectable in BIS during the 2019/2020 influenza season, while virtually no influenza viruses were found in BIS 2020/2021 during the COVID-19 pandemic.


Subject(s)
COVID-19/epidemiology , Influenza, Human/epidemiology , Sentinel Surveillance , COVID-19/diagnosis , Germany/epidemiology , Humans , Incidence , Influenza, Human/diagnosis , Oropharynx/virology , Orthomyxoviridae/classification , Orthomyxoviridae/genetics , Orthomyxoviridae/isolation & purification , RNA, Viral/genetics , Retrospective Studies , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Seasons
17.
J Infect Dev Ctries ; 15(10): 1408-1414, 2021 10 31.
Article in English | MEDLINE | ID: covidwho-1518651

ABSTRACT

INTRODUCTION: In this study, we aimed investigate the relationship of SARS-CoV-2 viral load cycle threshold (Ct) values with pneumonia. METHODOLOGY: A total of 158 patients in whom SARS-CoV-2 was confirmed in upper respiratory tract (URT) samples with molecular method and who had computed tomography (CT) of the chest, between April 2020 and June 2020 were included in this retrospective cross-sectional study. RESULTS: Mean age of 158 PCR positive patients was 45.22 ± 17.89 and 60.8% of them were male. Pneumonia was detected in 40.5% of the patients on their chest CT. A weak but significant correlation was found between SARS-CoV-2 Ct value detected with PCR in analysis of oropharyngeal/ nasopharyngeal (OP/NP) samples and chest CT score (Pearson's r: 0.197, p = 0.01). No correlation was found between the first detected viral load Ct value and age, gender and mortality. There was no significant correlation between chest CT score and mortality. While the areas remaining under ROC curve for Ct value in analysis of OP/NP samples in prediction of chest CT score ≥ 1, ≥ 5 and ≥ 10 were 0.564, 0.640 and 0.703 respectively. CONCLUSIONS: We found that the amount of SARS-CoV-2 viral load (inverse relationship with Ct) detected in OP/NP samples of patients with COVID-19 pneumonia did not reflect the increasing severity of pulmonary lesions on chest CT. Although primary target of SARS-CoV-2 is all epithelial cells of the respiratory tract we believe studies comparing viral loads in lower respiratory tract samples are needed to determine the severity of pulmonary disease.


Subject(s)
COVID-19/virology , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Viral Load/methods , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/diagnostic imaging , Child , Child, Preschool , Cross-Sectional Studies , Female , Humans , Lung/diagnostic imaging , Lung/pathology , Lung/virology , Male , Middle Aged , Nasopharynx/virology , Oropharynx/diagnostic imaging , Retrospective Studies , Tomography, X-Ray Computed , Young Adult
18.
Sci Rep ; 11(1): 22214, 2021 11 15.
Article in English | MEDLINE | ID: covidwho-1517639

ABSTRACT

Rapid nucleic-acid based tests that can be performed by non-professionals outside laboratory settings could help the containment of the pandemic SARS-CoV-2 virus and may potentially prevent further widespread lockdowns. Here, we present a novel compact portable detection instrument (the Egoo Health System) for extraction-free detection of SARS-CoV-2 using isothermal reverse transcription strand invasion based amplification (RT-SIBA). The SARS-CoV-2 RT-SIBA assay can be performed directly on crude oropharyngeal swabs without nucleic acid extraction with a reaction time of 30 min. The Egoo Health system uses a capsule system, which is automatically sealed tight in the Egoo instrument after applying the sample, resulting in a closed system optimal for molecular isothermal amplification. The performance of the Egoo Health System is comparable to the PCR instrument with an analytical sensitivity of 25 viral RNA copies per SARS-CoV-2 RT-SIBA reaction and a clinical sensitivity and specificity between 87.0-98.4% and 96.6-98.2% respectively.


Subject(s)
COVID-19/diagnosis , COVID-19/epidemiology , Equipment Design , Molecular Diagnostic Techniques/instrumentation , Molecular Diagnostic Techniques/methods , Pandemics/prevention & control , Reverse Transcriptase Polymerase Chain Reaction/instrumentation , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , COVID-19/virology , Cell Phone , Humans , Mobile Applications , Oropharynx/virology , Point-of-Care Testing , Polymorphism, Single Nucleotide , RNA, Viral/genetics , Retrospective Studies , Sensitivity and Specificity
19.
Emerg Microbes Infect ; 10(1): 2090-2097, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1479918

ABSTRACT

Since December 2019, coronavirus disease 2019 (COVID-19) caused by SARS coronavirus 2 (SARS-CoV-2) has spread and threatens public health worldwide. The recurrence of SARS-CoV-2 RNA detection in patients after discharge from hospital signals a risk of transmission from such patients to the community and challenges the current discharge criteria of COVID-19 patients. A wide range of clinical specimens has been used to detect SARS-CoV-2. However, to date, a consensus has not been reached regarding the most appropriate specimens to use for viral RNA detection in assessing COVID-19 patients for discharge. An anal swab sample was proposed as the standard because of prolonged viral detection. In this retrospective longitudinal study of viral RNA detection in 60 confirmed COVID-19 patients, we used saliva, oropharyngeal/nasopharyngeal swab (O/N swab) and anal swab procedures from admission to discharge. The conversion times of saliva and anal swab were longer than that of O/N swab. The conversion time of hyper sensitive-CRP was the shortest and correlated with that of CT scanning and viral detection. Some patients were found to be RNA-positive in saliva while RNA-negative in anal swab while the reverse was true in some other patients, which indicated that false negatives were inevitable if only the anal swab is used for evaluating suitability for discharge. These results indicated that double-checking for viral RNA using multiple and diverse specimens was essential, and saliva could be a candidate to supplement anal swabs to reduce false-negative results and facilitate pandemic control.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Saliva/virology , Adult , Anal Canal/virology , False Negative Reactions , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Oropharynx/virology , Patient Discharge , RNA, Viral/analysis , Retrospective Studies , Young Adult
SELECTION OF CITATIONS
SEARCH DETAIL