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1.
Saudi Med J ; 43(1): 9-30, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1622887

ABSTRACT

OBJECTIVES: To evaluate the diagnostic utility of self-collected saliva in coronavirus desease-19 (COVID-19) screening procedures. METHODS: A total of 6 databases were reviewed from their inception until August 2021. Sensitivity and specificity were measured by extracting items (true-positive, true-negative, false-positive and false-negative) from each paper. We evaluated the diagnostic accuracy based on Quality Assessment of Diagnostic Accuracy Studies, version 2. RESULTS: A total of 41 studies were included in the final analysis. The diagnostic odds ratio (OR) of self-collected saliva was 196.2022 (95% confidence interval [CI]: 117.8833-326.5546). The area under the summary receiver operating characteristic curve was 0.955. For detecting COVID-19, self-collected saliva had a moderate sensitivity of 0.8476 [0.8045-0.8826] and positive predictive value of 0.9404 [0.9122-0.9599] but high specificity of 0.9817 [0.9707-0.9887] and negative predictive value of 0.9467 [0.9130-0.9678]. In a subgroup analysis, the diagnostic accuracy of self-collected saliva tended to be higher for symptomatic (vs. asymptomatic) examinees. CONCLUSION: Although naso/oropharyngeal swab tests are the most accurate and important diagnostic tools, the saliva-based testing method can be used as a suitable alternative test, with the advantages of increased patient convenience, efficient testing, and the need for fewer medical staff and resources. In particular, simple collecting method such as drooling or spitting without coughing would be effective in evaluating the symptomatic patients.PROSPERO no.: CRD42021279287.


Subject(s)
COVID-19 , Saliva , Humans , Nasopharynx , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2 , Sensitivity and Specificity , Specimen Handling
4.
JAMA Netw Open ; 5(1): e2142057, 2022 01 04.
Article in English | MEDLINE | ID: covidwho-1604871

ABSTRACT

Importance: Closure of day care centers has been implemented globally to contain the COVID-19 pandemic but has negative effects on children's health and psychosocial well-being. Objective: To investigate the feasibility of surveillance among children and childcare workers and to model the efficacy of surveillance on viral spread prevention. Design, Setting, and Participants: This nonrandomized controlled trial was conducted at 9 day care centers in Wuerzburg, Germany, from October 2020 to March 2021. Participants included children attending day care, childcare workers, and household members. Participating day care centers were assigned to different surveillance modules in a nonrandomized feasibility study. A mathematical model for SARS-CoV-2 spread in day care centers was developed to identify optimal surveillance. Interventions: Modules 1, 2, and 3 involved continuous surveillance of asymptomatic children and childcare workers by SARS-CoV-2 polymerase chain reaction testing of either midturbinate nasal swabs twice weekly (module 1) or once weekly (module 2) or self-sampled saliva samples twice weekly (module 3). Module 4 involved symptom-based, on-demand testing of children, childcare workers, and their household members by oropharyngeal swabs. All participants underwent SARS-CoV-2 antibody status testing before and after the sampling period. Questionnaires on attitudes and perception of the pandemic were administered in weeks 1, 6, and 12. Mathematical modeling was used to estimate SARS-CoV-2 spread in day care centers. Main Outcomes and Measures: The primary outcomes were acceptance of the respective surveillance protocols (feasibility study) and the estimated number of secondary infections (mathematical modeling). Results: Of 954 eligible individuals (772 children and 182 childcare workers), 592 (62%), including 442 children (median [IQR] age, 3 [2-4] years; 214 [48.6%] female) and 150 childcare workers (median [IQR] age, 29 [25-44] years; 129 [90.8%] female) participated in the surveillance. In total, 4755 tests for SARS-CoV-2 detected 2 infections (1 childcare worker and 1 adult household member). Acceptance for continuous surveillance was highest for biweekly saliva testing (150 of 221 eligible individuals [67.9%; 95% CI, 61.5%-73.7%]) compared with biweekly (51 of 117 individuals [43.6%; 95% CI, 35.0%-52.6%]) and weekly (44 of 128 individuals [34.4%; 95% CI, 26.7%-43.0%]) midturbinate swabbing (P < .001). Dropout rates were higher for midturbinate swabbing (biweekly, 11 of 62 participants [18%]; once weekly, 11 of 55 participants [20%]) than for saliva testing (6 of 156 participants [4%]). Mathematical modeling based on study and literature data identified biweekly testing of at least 50% of children and childcare workers as minimal requirements to limit secondary infections. Conclusions and Relevance: In this nonrandomized controlled trial, surveillance for SARS-CoV-2 in 9 German day care centers was feasible and well accepted. Mathematical modeling estimated that testing can minimize the spread of SARS-CoV-2 in day care centers. These findings enable setup of surveillance programs to maintain institutional childcare. Trial Registration: German Registry for Clinical Trials Identifier: DRKS00023721.


Subject(s)
COVID-19 Testing , COVID-19/prevention & control , Caregivers , Child Care , Child Day Care Centers , Child Health , Adult , COVID-19/diagnosis , COVID-19/virology , Child , Child, Preschool , Feasibility Studies , Female , Germany , Humans , Male , Models, Theoretical , Pandemics , Patient Acceptance of Health Care , Polymerase Chain Reaction , SARS-CoV-2 , Saliva , Specimen Handling
5.
Front Public Health ; 9: 789402, 2021.
Article in English | MEDLINE | ID: covidwho-1607927

ABSTRACT

Repeated testing of a population is critical for limiting the spread of the SARS-CoV-2 virus and for the safe reopening of educational institutions such as kindergarten-grade 12 (K-12) schools and colleges. Many screening efforts utilize the CDC RT-PCR based assay which targets two regions of the novel Coronavirus nucleocapsid gene. The standard approach of testing each person individually, however, poses a financial burden to these institutions and is therefore a barrier to using testing for re-opening. Pooling samples from multiple individuals into a single test is an attractive alternate approach that promises significant cost savings-however the specificity and sensitivity of such approaches needs to be assessed prior to deployment. To this end, we conducted a pilot study to evaluate the feasibility of analyzing samples in pools of eight by the established RT-PCR assay. Participants (1,576) were recruited from amongst the Tufts University community undergoing regular screening. Each volunteer provided two swabs, one analyzed separately and the other in a pool of eight. Because the positivity rate was very low, we spiked approximately half of the pools with laboratory-generated swabs produced from known positive cases outside the Tufts testing program. The results of pooled tests had 100% correspondence with those of their respective individual tests. We conclude that pooling eight samples does not negatively impact the specificity or sensitivity of the RT-PCR assay and suggest that this approach can be utilized by institutions seeking to reduce surveillance costs.


Subject(s)
COVID-19 , RNA, Viral , Humans , Pilot Projects , SARS-CoV-2 , Schools , Specimen Handling
6.
Emerg Microbes Infect ; 11(1): 250-259, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1585240

ABSTRACT

Testing and vaccination have been major components of the strategy for combating the ongoing COVID-19 pandemic. In this study, we have developed a quantitative anti-SARS-CoV-2 spike (S1) IgG antibody assay using a fingerstick dried blood sample. We evaluated the feasibility of using this high-throughput and quantitative anti-SARS-CoV-2 spike (S1) IgG antibody testing assay in vaccinated individuals. Fingerstick blood samples were collected and analyzed from 137 volunteers before and after receiving the Moderna or Pfizer mRNA vaccine. Anti-SARS-CoV-2 S1 IgG antibody could not be detected within the first 7 days after receiving the first vaccine dose, however, the assay reliably detected antibodies from day 14 onwards. In addition, no anti-SARS-CoV-2 nucleocapsid (N) protein IgG antibody was detected in any of the vaccinated or healthy participants, indicating that the anti-SARS-CoV-2 S1 IgG assay is specific for the mRNA vaccine-induced antibodies. The S1 IgG levels detected in fingerstick samples correlated with the levels found in venous blood plasma samples and with the efficacy of venous blood plasma samples in the plaque reduction neutralization test (PRNT). The assay displayed a limit of quantification (LOQ) of 0.59 µg/mL and was found to be linear in the range of 0.51-1000 µg/mL. Finally, its clinical performance displayed a Positive Percent Agreement (PPA) of 100% (95% CI: 0.89-1.00) and a Negative Percent Agreement (NPA) of 100% (95% CI: 0.93-1.00). In summary, the assay described here represents a sensitive, precise, accurate, and simple method for the quantitative detection and monitoring of post-vaccination anti-SARS-CoV-2 spike IgG responses.


Subject(s)
COVID-19 Serological Testing/methods , COVID-19 Vaccines/immunology , COVID-19/immunology , High-Throughput Screening Assays/methods , Immunoassay/methods , SARS-CoV-2/immunology , Specimen Handling/methods , Antibodies, Viral/blood , Female , Humans , Immunoglobulin G/blood , Male , Spike Glycoprotein, Coronavirus , Vaccination
7.
Front Public Health ; 9: 743300, 2021.
Article in English | MEDLINE | ID: covidwho-1581123

ABSTRACT

In January 2021, the Chilean city of Concepción experienced a second wave of coronavirus 2019 (COVID-19) while in early April 2021, the entire country faced the same situation. This outbreak generated the need to modify and validate a method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva, thereby expanding the capacity and versatility of testing for COVID-19. This study was conducted in February 2021 in the Chilean city of Concepción during which time, the town was under total quarantine. The study participants were mostly symptomatic (87.4%), not hospitalized, and attended care centers because of their health status rather than being asked by the researchers. People coming to the health center in Concepción to be tested for COVID-19 (via reverse transcriptase polymerase chain reaction [RT-PCR]) from a specimen of nasopharyngeal swab (NPS) were then invited to participate in this study. A total of 131 participants agreed to sign an informed consent and to provide saliva and NPS specimens to validate a method in terms of sensitivity, specificity, and statistical analysis of the cycle threshold (Ct) values from the RT-PCR. Calculations pertaining to the 127 participants who were ultimately included in the analysis showed sensitivity and specificity at 94.34% (95% CI: 84.34-98.82%) and 98.65% (95% CI: 92.70-99.97%), respectively. The saliva specimen showed a performance comparable to NPS as demonstrated by the diagnostic parameters. This RT-PCR method from the saliva specimen is a highly sensitive and specific alternative compared to the reference methodology, which uses the NPS specimen. This modified and validated method is intended for use in the in vitro diagnosis of SARS-CoV-2, which provides health authorities in Chile and local laboratories with a real testing alternative to RT-PCR from NPS.


Subject(s)
COVID-19 , SARS-CoV-2 , Saliva/virology , COVID-19/diagnosis , COVID-19 Testing , Chile , Humans , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , Specimen Handling
8.
Biosens Bioelectron ; 200: 113909, 2022 Mar 15.
Article in English | MEDLINE | ID: covidwho-1588211

ABSTRACT

Coronavirus disease 2019 (COVID-19) has been recognized as a global pandemic outbreak, opening the most severe socio-economic crisis since World War II. Different scientific activities have been emerged in this global scenario, including the development of innovative analytical tools to measure nucleic acid, antibodies, and antigens in the nasopharyngeal swab, serum, and saliva for prompt identification of COVID-19 patients and to evaluate the immune response to the vaccine. The detection of SARS-CoV-2 in saliva remains a challenge for the lack of sufficient sensitivity. To address this issue, we developed a novel paper-based immunoassay using magnetic beads to support the immunological chain and 96-well wax-printed paper plate as a platform for color visualization by using a smartphone combined with Spotxel free-charge app. To assess the reliability of the measurement of SARS-CoV-2 in saliva, untreated saliva was used as a specimen and the calibration curve demonstrated a dynamic range up to 10 µg/mL, with a detection limit equal to 0.1 µg/mL. The effectiveness of this sustainable analytical tool in saliva was evaluated by comparing the data with the nasopharyngeal swab specimens sampled by the same patients and tested with Real-Time PCR reference method, founding 100% of agreement, even in the case of high Cycle Threshold (CT) numbers (low viral load). Furthermore, the positive saliva samples were characterized by the next-generation sequencing method, demonstrating the capability to detect the Delta variant, which is actually (July 2021) the most relevant variant of concern.


Subject(s)
Biosensing Techniques , COVID-19 , Colorimetry , Humans , Immunoassay , Magnetic Phenomena , Nasopharynx , Reproducibility of Results , SARS-CoV-2 , Saliva , Smartphone , Specimen Handling
9.
Infect Control Hosp Epidemiol ; 42(11): 1340-1344, 2021 11.
Article in English | MEDLINE | ID: covidwho-1574695

ABSTRACT

BACKGROUND: Widespread testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) is necessary to curb the spread of coronavirus disease 2019 (COVID-19), but testing is undermined when the only option is a nasopharyngeal swab. Self-collected swab techniques can overcome many of the disadvantages of a nasopharyngeal swab, but they require evaluation. METHODS: Three self-collected non-nasopharyngeal swab techniques (saline gargle, oral swab and combined oral-anterior nasal swab) were compared to a nasopharyngeal swab for SARS-CoV-2 detection at multiple COVID-19 assessment centers in Toronto, Canada. The performance characteristics of each test were assessed. RESULTS: The adjusted sensitivity of the saline gargle was 0.90 (95% CI 0.86-0.94), the oral swab was 0.82 (95% CI, 0.72-0.89) and the combined oral-anterior nasal swab was 0.87 (95% CI, 0.77-0.93) compared to a nasopharyngeal swab, which demonstrated a sensitivity of ˜90% when all positive tests were the reference standard. The median cycle threshold values for the SARS-CoV-2 E-gene for concordant and discordant saline gargle specimens were 17 and 31 (P < .001), for the oral swabs these values were 17 and 28 (P < .001), and for oral-anterior nasal swabs these values were 18 and 31 (P = .007). CONCLUSIONS: Self-collected saline gargle and an oral-anterior nasal swab have a similar sensitivity to a nasopharyngeal swab for the detection of SARS-CoV-2. These alternative collection techniques are cheap and can eliminate barriers to testing, particularly in underserved populations.


Subject(s)
COVID-19 , Outpatients , Humans , Nasopharynx , SARS-CoV-2 , Saliva , Specimen Handling
10.
J Infect Dev Ctries ; 15(11): 1640-1645, 2021 11 30.
Article in English | MEDLINE | ID: covidwho-1572709

ABSTRACT

INTRODUCTION: To analyze the virus spread among Sassari Hospital staff in the first Covid-19 wave and the impact of the Swab Team, a multidisciplinary task force entitled of nasopharyngeal swab collection and testing. METHODOLOGY: Nasopharyngeal swabs from HCWs between March 6 and May 28 2020 are evaluated. RESULTS: 4919 SARS-CoV-2 tests were performed on 3521 operators. Nurses and doctors are the categories at highest risk. After the Swab Team institution, the average number of swabs raised from 47/day to 86/day (p = 0.007). Positive samples decreased from 18.6% to 1.7% (p < 0.0001). CONCLUSIONS: The Swab Team is effective in increasing the cases tested and in reducing the reporting time. Procedure standardization reduces the risk for all the subjects involved (no transmission among swab team members, nor during the sample collection).


Subject(s)
COVID-19/prevention & control , Medical Staff, Hospital , Occupational Diseases/prevention & control , Patient Care Team , SARS-CoV-2 , Specimen Handling , Adult , COVID-19/diagnosis , COVID-19/epidemiology , Female , Humans , Italy/epidemiology , Male , Middle Aged , Pandemics , Retrospective Studies
11.
PLoS One ; 16(12): e0260187, 2021.
Article in English | MEDLINE | ID: covidwho-1571986

ABSTRACT

To date, there is limited information about the presence of SARS-CoV-2 in semen especially in the acute phase of the infection. While available data from cohort studies including a total of 342 patients in the acute or recovery phase of the infection are reassuring, one study mentioned detecting virus in the semen of 6/38 COVID-19 patients. Here we assessed SARS-CoV-2 presence in the semen of COVID-19 positive patients in the acute stage of infection, within 24 hours of the positive nasopharyngeal swabs. Semen, seminal plasma and spermatozoa pellet were screened for SARS-CoV-2 and manual or airborne contamination during semen sampling. Among the 32 COVID-19 volunteers, the median interval from the onset of symptoms to semen collection was 4 days [IQR: 0-8]. Only one presented positive SARS-CoV-2 PCR in semen and seminal plasma fractions, although the spermatozoa pellet was negative. Viral cultures were all negative. We observed slightly higher concentrations of bacterial DNA in the SARS-CoV-2 positive specimen than in all negative samples. The bacteria identified neither confirm nor rule out contamination by oropharyngeal secretions during collection. SARS-CoV-2 was rarely present in semen during the acute phase of the disease. This very rare situation could be connected to oral or manual contamination during semen collection. The possible presence of SARS-CoV-2 in semen calls for nasopharyngeal viral testing and strict hygiene protocols during semen collection before assisted reproductive attempts.


Subject(s)
COVID-19/virology , SARS-CoV-2/isolation & purification , Semen/chemistry , Spermatozoa/chemistry , Adult , Humans , Male , Middle Aged , Nasopharynx/virology , Semen/virology , Specimen Handling , Spermatozoa/virology
12.
ACS Appl Mater Interfaces ; 13(50): 60612-60624, 2021 Dec 22.
Article in English | MEDLINE | ID: covidwho-1569206

ABSTRACT

New analytical techniques that overcome major drawbacks of current routinely used viral infection diagnosis methods, i.e., the long analysis time and laboriousness of real-time reverse-transcription polymerase chain reaction (qRT-PCR) and the insufficient sensitivity of "antigen tests", are urgently needed in the context of SARS-CoV-2 and other highly contagious viruses. Here, we report on an antifouling terpolymer-brush biointerface that enables the rapid and sensitive detection of SARS-CoV-2 in untreated clinical samples. The developed biointerface carries a tailored composition of zwitterionic and non-ionic moieties and allows for the significant improvement of antifouling capabilities when postmodified with biorecognition elements and exposed to complex media. When deployed on a surface of piezoelectric sensor and postmodified with human-cell-expressed antibodies specific to the nucleocapsid (N) protein of SARS-CoV-2, it made possible the quantitative analysis of untreated samples by a direct detection assay format without the need of additional amplification steps. Natively occurring N-protein-vRNA complexes, usually disrupted during the sample pre-treatment steps, were detected in the untreated clinical samples. This biosensor design improved the bioassay sensitivity to a clinically relevant limit of detection of 1.3 × 104 PFU/mL within a detection time of only 20 min. The high specificity toward N-protein-vRNA complexes was validated both by mass spectrometry and qRT-PCR. The performance characteristics were confirmed by qRT-PCR through a comparative study using a set of clinical nasopharyngeal swab samples. We further demonstrate the extraordinary fouling resistance of this biointerface through exposure to other commonly used crude biological samples (including blood plasma, oropharyngeal, stool, and nasopharyngeal swabs), measured via both the surface plasmon resonance and piezoelectric measurements, which highlights the potential to serve as a generic platform for a wide range of biosensing applications.


Subject(s)
COVID-19 Testing , COVID-19/diagnosis , Coronavirus Nucleocapsid Proteins/chemistry , Nasal Mucosa/virology , Polymers/chemistry , RNA, Viral/metabolism , SARS-CoV-2 , Biofouling , Biological Assay , Biosensing Techniques , Humans , Ions , Limit of Detection , Mass Spectrometry , Nasopharynx/virology , Phosphoproteins/chemistry , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Specimen Handling
13.
Clin Infect Dis ; 73(9): e3106-e3109, 2021 11 02.
Article in English | MEDLINE | ID: covidwho-1565979

ABSTRACT

We compared self-collected oral fluid swab specimens with and without clinician supervision, clinician-supervised self-collected anterior nasal swab specimens, and clinician-collected nasopharyngeal swab specimens for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Supervised oral fluid and nasal swab specimens performed similarly to clinician-collected nasopharyngeal swab specimens. No sample type could detect SARS-CoV-2 infections amongst all positive participants.


Subject(s)
COVID-19 , Humans , Nasopharynx , SARS-CoV-2 , Saliva , Specimen Handling
14.
J Clin Virol ; 146: 105053, 2022 01.
Article in English | MEDLINE | ID: covidwho-1561863

ABSTRACT

Throughout the ongoing SARS-CoV-2 pandemic, the recommended sample type for initial diagnostic testing for SARS-CoV-2 infection has been a nasopharyngeal swab. Shortages in swabs and difficulties in obtaining nasopharyngeal swabs in certain patient groups has prompted research into alternative specimen types for the diagnosis of COVID-19. The aim of this study was to assess how 'simply collected' saliva along with tongue swabs and buccal swabs preformed as an alternative specimen type for SARS-CoV-2 detection. It was observed that saliva samples allowed for the detection of 85.3% of positive patients, tongue swabs allowed for the detection of 67.6% of positive patients and buccal swabs allowed for detection of 20.8% of positive patients, when compared to nasopharyngeal swabs. From this data, it could be concluded that using simple saliva collection can provide a less invasive and reliable alternative method for the detection of SARS-CoV2 particularly in those patients where invasive sampling is difficult and where regular repeat testing is required.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , Nasopharynx , RNA, Viral , Saliva , Specimen Handling , Tongue
15.
J Med Virol ; 93(12): 6693-6695, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1544321

ABSTRACT

We aimed to compare reverse transcription-polymerase chain reaction (RT-PCR) results of nasopharyngeal aspiration (NA) and nasopharyngeal swab (NS) samples in the diagnosis of coronavirus disease 2019. NS was obtained with a dacron swab and NA was performed by aspiration cannula. The sampling was performed by an otolaryngologist to ensure standardized correct sampling from the nasopharynx. RT-PCR was performed for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The level of agreement between the result of NA and NS samples for each patient was analyzed. The Ct values were compared. Thirty-three patients were enrolled in the study with a mean age of 56.3 years. Thirteen subjects resulted negative with both NS and NA; 20 subjects resulted positive with NA and 18 subjects resulted positive with NS. The mean values of Ct for NA samples and NS samples were 24.6 ± 5.9 and 24 ± 6.7, respectively. There was no statistical difference between Ct values of NA and NS samples (p = 0.48). RT-PCR for SARS-Cov2 performed with NA sample and NS sample showed a strong correlation regarding the positivity/negativity and the Ct values.


Subject(s)
COVID-19 Testing/methods , Nasopharynx/virology , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2 , Specimen Handling/methods , Adult , Aged , Female , Humans , Male , Middle Aged , Reproducibility of Results , Sensitivity and Specificity
16.
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
17.
J Med Virol ; 93(12): 6808-6812, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1544312

ABSTRACT

Real-time polymerase chain reaction (PCR) for SARS-CoV-2 is the mainstay of COVID-19 diagnosis, yet there are conflicting reports on its diagnostic performance. Wide ranges of false-negative PCR tests have been reported depending on clinical presentation, the timing of testing, specimens tested, testing method, and reference standard used. We aimed to estimate the frequency of discordance between initial nasopharyngeal (NP) PCR and repeat NP sampling PCR and serology in acutely ill patients admitted to the hospital. Panel diagnosis of COVID-19 infection is further utilized in discordance analysis. Included in the study were 160 patients initially tested by NP PCR with repeat NP sampling PCR and/or serology performed. The percent agreement between initial and repeat PCR was 96.7%, while the percent agreement between initial PCR and serology was 98.9%. There were 5 (3.1%) cases with discordance on repeat testing. After discordance analysis, 2 (1.4%) true cases tested negative on initial PCR. Using available diagnostic methods, discordance on repeat NP sampling PCR and/or serology is a rare occurrence.


Subject(s)
COVID-19/diagnosis , COVID-19/virology , Nasopharynx/virology , SARS-CoV-2/genetics , Adult , COVID-19 Testing/methods , Female , Humans , Male , Real-Time Polymerase Chain Reaction/methods , Reference Standards , Reverse Transcriptase Polymerase Chain Reaction/methods , Sensitivity and Specificity , Specimen Handling/methods
19.
20.
J Med Virol ; 93(12): 6575-6581, 2021 12.
Article in English | MEDLINE | ID: covidwho-1530180

ABSTRACT

Reliable and rapid detection of severe acute respiratory syndrome coronavirus 2 in laboratory setting is critical to control the pandemic. We aimed to an evaluated polymerase chain reaction (PCR) efficiency of nasopharyngeal swabs stored in viral transport medium (VTM) in different temperatures. Ninety swabs taken into VTM were analyzed at the first hour, then divided into two groups with similar numbers of positive and negative samples. Positive samples of each group were also subgrouped according to Fam CT values as low CT (<25), medium CT (25-32), and high CT (32-38) groups. One group was stored at 4°C, while the other was stored at room temperature, PCR analyses were repeated every 24 h for 5 days and on Day 12. There was a total of 30 positive samples (12 low CT, 11 medium CT, and 7 high CT). The CT values of both groups remained unchanged in first 3 days while the CT values of the room temperature group increased after the third day. All of the positive samples remained positive in both groups for the first 5 days. On the 12th day, the total number of positives decreased to 8 in the room temperature group and 11 in the 4°C groups. All the low CT samples remained positive in both groups. In conclusion, it is safe to store positive samples in room temperature for up to 5 days. Only samples with high viral loads remain positive for 12 days, regardless of whether stored at room temperature or 4°C. Negative samples don't turn to invalid if stored in VTM.


Subject(s)
COVID-19 Testing/methods , Real-Time Polymerase Chain Reaction/methods , Specimen Handling/methods , COVID-19/diagnosis , Humans , Real-Time Polymerase Chain Reaction/standards , SARS-CoV-2 , Specimen Handling/standards , Time Factors
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