Clinical performance of SARS-CoV-2 detection on the cobas Liat using water gargle samples.

Spring water gargle (SWG) is a suitable, non-invasive, alternative specimen for SARS-CoV-2 detection by RT-PCR. This study sought to evaluate the performance of the cobas Liat point-of-care system for the detection of SARS-CoV-2 in SWG samples. SWG samples and standard oral and nasopharyngeal swab (ONPS) were collected simultaneously from participants in a COVID-19 screening clinic, in November and December 2020. Both sample types were analyzed in parallel on the cobas Liat platform and with the Seegene Allplex 2019-nCoV assay. Among the 110 participants, 53% had compatible symptoms and 71% had a contact with a confirmed COVID-19 case. Only two (1.8%) individuals had neither symptoms nor contact. Amongst 110 paired samples, 25 (23%) were positive for SARS-CoV-2 on the cobas Liat for a least one sample type, with a kappa coefficient of 0.92. Agreement between the cobas Liat platform and the Seegene assay was also excellent (kappa coefficient values of 0.94 and 0.95). Two SWG samples failed to provide a positive result when their ONPS pair was positive, but their cycle threshold (Ct) values were >35 on the Seegene assay, reflecting a low viral load. Overall, the performance of the cobas Liat platform is excellent for the detection of SARS-CoV-2 in SWG samples in a high pre-test probability population.

Evaluation of Real-life Use of Point-of-care Rapid Antigen Testing for SARS-CoV-2 in Schools (EPOCRATES): a cohort study.

BACKGROUND: SARS-CoV-2 transmission has an impact on education. In this study, we assessed the performance of rapid antigen detection tests (RADTs) versus polymerase chain reaction (PCR) for the diagnosis of SARS-CoV-2 infection in school settings, and RADT use for monitoring exposed contacts. METHODS: In this real-world, prospective observational cohort study, high-school students and staff were recruited from 2 high schools in Montréal, Canada, and followed from Jan. 25 to June 10, 2021. Twenty-five percent of asymptomatic participants were tested weekly by RADT (nasal) and PCR (gargle). Class contacts of cases were tested. Symptomatic participants were tested by RADT (nasal) and PCR (nasal and gargle). The number of cases and outbreaks were compared with those of other high schools in the same area. RESULTS: Overall, 2099 students and 286 school staff members consented to participate. The overall specificity of RADTs varied from 99.8% to 100%, with a lower sensitivity, varying from 28.6% in asymptomatic to 83.3% in symptomatic participants. Secondary cases were identified in 10 of 35 classes. Returning students to school after a 7-day quarantine, with a negative PCR result on days 6-7 after exposure, did not lead to subsequent outbreaks. Of cases for whom the source was known, 37 of 51 (72.5%) were secondary to household transmission, 13 (25.5%) to intraschool transmission, and 1 to community contacts between students in the same school. INTERPRETATION: Rapid antigen detection tests did not perform well compared with PCR in asymptomatic individuals. Reinforcing policies for symptom screening when entering schools and testing symptomatic individuals with RADTs on the spot may avoid subsequent substantial exposures in class. Preprint: medRxiv - doi.org/10.1101/2021.10.13.21264960.

Outcomes of hospitalized COVID-19 patients in Canada: impact of ethnicity, migration status and country of birth.

BACKGROUND: Ethnoracial groups in high-income countries have a 2-fold higher risk of SARS-CoV-2 infection, associated hospitalizations, and mortality than Whites. Migrants are an ethnoracial subset that may have worse COVID-19 outcomes due to additional barriers accessing care, but there are limited data on in-hospital outcomes. We aimed to disaggregate and compare COVID-19 associated hospital outcomes by ethnicity, immigrant status and region of birth. METHODS: Adults with community-acquired SARS-CoV-2 infection, hospitalized March 1-June 30, 2020, at four hospitals in Montréal, Quebec, Canada, were included. Age, sex, socioeconomic status, comorbidities, migration status, region of birth, self-identified ethnicity [White, Black, Asian, Latino, Middle East/North African], intensive care unit (ICU) admissions and mortality were collected. Adjusted hazard ratios (aHR) for ICU admission and mortality by immigrant status, ethnicity and region of birth adjusted for age, sex, socioeconomic status and comorbidities were estimated using Fine and Gray competing risk models. RESULTS: Of 1104 patients (median [IQR] age, 63.0 [51.0-76.0] years; 56% males), 57% were immigrants and 54% were White. Immigrants were slightly younger (62 vs 65 years; p = 0.050), had fewer comorbidities (1.0 vs 1.2; p < 0.001), similar crude ICU admissions rates (33.0% vs 28.2%) and lower mortality (13.3% vs 17.6%; p < 0.001) than Canadian-born. In adjusted models, Blacks (aHR 1.39, 95% confidence interval 1.05-1.83) and Asians (1.64, 1.15-2.34) were at higher risk of ICU admission than Whites, but there was significant heterogeneity within ethnic groups. Asians from Eastern Asia/Pacific (2.15, 1.42-3.24) but not Southern Asia (0.97, 0.49-1.93) and Caribbean Blacks (1.39, 1.02-1.89) but not SSA Blacks (1.37, 0.86-2.18) had a higher risk of ICU admission. Blacks had a higher risk of mortality (aHR 1.56, p = 0.049). CONCLUSIONS: Data disaggregated by region of birth identified subgroups of immigrants at increased risk of COVID-19 ICU admission, providing more actionable data for health policymakers to address health inequities.

Clinical performance of SARS-CoV-2 detection on the cobas Liat using water gargle samples✰

Spring water gargle (SWG) is a suitable, non-invasive, alternative specimen for SARS-CoV-2 detection by RT-PCR. This study sought to evaluate the performance of the cobas Liat point-of-care system for the detection of SARS-CoV-2 in SWG samples. SWG samples and standard oral and nasopharyngeal swab (ONPS) were collected simultaneously from participants in a COVID-19 screening clinic, in November and December 2020. Both sample types were analyzed in parallel on the cobas Liat platform and with the Seegene Allplex 2019-nCoV assay. Among the 110 participants, 53% had compatible symptoms and 71% had a contact with a confirmed COVID-19 case. Only two (1.8%) individuals had neither symptoms nor contact. Amongst 110 paired samples, 25 (23%) were positive for SARS-CoV-2 on the cobas Liat for a least one sample type, with a kappa coefficient of 0.92. Agreement between the cobas Liat platform and the Seegene assay was also excellent (kappa coefficient values of 0.94 and 0.95). Two SWG samples failed to provide a positive result when their ONPS pair was positive, but their cycle threshold (Ct) values were >35 on the Seegene assay, reflecting a low viral load. Overall, the performance of the cobas Liat platform is excellent for the detection of SARS-CoV-2 in SWG samples in a high pre-test probability population.

In-hospital outcomes of SARS-CoV-2-infected health care workers in the COVID-19 pandemic first wave, Quebec, Canada.

BACKGROUND: Health care workers (HCW), particularly immigrants and ethnic minorities are at increased risk for SARS-CoV-2 infection. Outcomes during a COVID-19 associated hospitalization are not well described among HCW. We aimed to describe the characteristics of HCW admitted with COVID-19 including immigrant status and ethnicity and the associated risk factors for Intensive Care unit (ICU) admission and death. METHODS: Adults with laboratory-confirmed community-acquired COVID-19 hospitalized from March 1 to June 30, 2020, at four tertiary-care hospitals in Montréal, Canada were included. Demographics, comorbidities, occupation, immigration status, country of birth, ethnicity, workplace exposures, and hospital outcomes (ICU admission and death) were obtained through a chart review and phone survey. A Fine and Gray competing risk proportional hazards model was used to estimate the risk of ICU admission among HCW stratified by immigrant status and region of birth. RESULTS: Among 1104 included persons, 150 (14%) were HCW, with a phone survey participation rate of 68%. HCWs were younger (50 vs 64 years; p<0.001), more likely to be female (61% vs 41%; p<0.001), migrants (68% vs 55%; p<0.01), non-White (65% vs 41%; p<0.001) and healthier (mean Charlson Comorbidity Index of 0.3 vs 1.2; p<0.001) compared to non-HCW. They were as likely to be admitted to the ICU (28% vs 31%; p = 0.40) but were less likely to die (4% vs. 17%; p<0.001). Immigrant HCW accounted for 68% of all HCW cases and, compared to Canadian HCW, were more likely to be personal support workers (PSW) (54% vs. 33%, p<0.01), to be Black (58% vs 4%) and to work in a Residential Care Facility (RCF) (59% vs 33%; p = 0.05). Most HCW believed that they were exposed at work, 55% did not always have access to personal protective equipment (PPE) and 40% did not receive COVID-19-specific Infection Control (IPAC) training. CONCLUSION: Immigrant HCW were particularly exposed to COVID-19 infection in the first wave of the pandemic in Quebec. Despite being young and healthy, one third of all HCW required ICU admission, highlighting the importance of preventing workplace transmission through strong infection prevention and control measures, including high COVID-19 vaccination coverage.

Evaluation of water gargle samples for SARS-CoV-2 detection using Abbott ID NOW COVID-19 assay.

The Abbott ID NOW™ COVID-19 assay has been shown as a reliable and sensitive alternative to reverse transcription-polymerase chain reaction (RT-PCR) testing from nasopharyngeal or nasal samples in symptomatic patients. Water gargle is an acceptable noninvasive alternative specimen for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) detection by RT-PCR. The objective of this study was to evaluate the performance of water gargle samples for the detection of SARS-CoV-2 using the ID NOW. Residual gargle samples were randomly selected among positive standard of care (SOC)-nucleic acid amplification test (NAAT) samples. For testing on ID NOW, the manufacturer's instructions were followed, except for the specimen addition step: 500 µl of the gargle specimen was added to the blue sample receiver with a pipette and gently mixed. Among the 202 positive samples by SOC-NAAT, 185 were positive by ID NOW (positive percent agreement [PPA]) = 91.6% (95% confidence interval [CI]: 86.9-95.0). For the 17 discordant samples, cycle threshold (Ct ) values were all ≥31.0. The PPA was significantly lower among asymptomatic patients (84.4%; 95% CI: 73.2-92.3) versus symptomatic patients (95.2%; 95% CI: 89.8-98.2). The performance of the ID NOW for the detection of SARS-CoV-2 infection on gargle samples is excellent when Ct values are <31.0 and for patients that have COVID-19 compatible symptoms.

Natural spring water gargle samples as an alternative to nasopharyngeal swabs for SARS-CoV-2 detection using a laboratory-developed test.

The objective of this study was to validate the use of spring water gargle (SWG) as an alternative to oral and nasopharyngeal swab (ONPS) for SARS-CoV-2 detection with a laboratory-developed test. Healthcare workers and adults from the general population, presenting to one of two COVID-19 screening clinics in Montréal and Québec City, were prospectively recruited to provide a gargle sample in addition to the standard ONPS. The paired specimens were analyzed using thermal lysis followed by a laboratory-developed nucleic acid amplification test (LD-NAAT) to detect SARS-CoV-2, and comparative performance analysis was performed. An individual was considered infected if a positive result was obtained on either sample. A total of 1297 adult participants were recruited. Invalid results (n = 18) were excluded from the analysis. SARS-CoV-2 was detected in 144/1279 (11.3%) participants: 126 from both samples, 15 only from ONPS, and 3 only from SWG. Overall, the sensitivity was 97.9% (95% CI: 93.7-99.3) for ONPS and 89.6% (95% CI: 83.4-93.6; p = 0.005) for SWG. The mean ONPS cycle threshold (Ct ) value was significantly lower for the concordant paired samples as compared to discordant ones (22.9 vs. 32.1; p < 0.001). In conclusion, using an LD-NAAT with thermal lysis, SWG is a less sensitive sampling method than the ONPS. However, the higher acceptability of SWG might enable a higher rate of detection from a population-based perspective. Nonetheless, in patients with a high clinical suspicion of COVID-19, a repeated analysis with ONPS should be considered. The sensitivity of SWG using NAAT preceded by chemical extraction should be evaluated.

Outcomes of hospital-acquired SARS-CoV-2 infection in the Canadian first wave epicentre: a retrospective cohort study.

BACKGROUND: During the first wave of the COVID-19 pandemic, a substantial number of Quebec hospitals were hit by hospital-acquired (HA) SARS-CoV-2 infections. Our objective was to assess whether mortality is higher in HA cases than in non-hospital-acquired (NHA) cases and determine the prevalence of HA-SARS-CoV-2 infection in our hospital. METHODS: This retrospective single-centre cohort study included all adults (≥ 18 yr) who had COVID-19, admitted to Hôpital Maisonneuve-Rosemont (Montréal, Canada) from Mar. 1 to June 30, 2020. We collected data on demographic characteristics, comorbidities, treatment, admission to the intensive care unit (ICU) and mechanical ventilation requirements from electronic health records. We adjudicated hospital acquisition based on the timing of symptom onset, and polymerase chain reaction testing for and exposures to SARS-CoV-2. To evaluate the association between HA-SARS-CoV-2 infection and in-hospital mortality, we computed a multivariable logistic regression analysis including known risk factors for death in patients with COVID-19 as covariates. RESULTS: Among 697 patients with SARS-CoV-2 infection, 253 (36.3%) were classified as HA. The mortality rate was higher in the HA group than in the NHA group (38.2% v. 26.4%, p = 0.001), while the rates of ICU admission (8.3% v. 19.1%, p = 0.001) and requirement for mechanical ventilation (3.6% v. 13.0%, p = 0.001) were lower. Multivariable logistic regression analysis showed that HA-SARS-CoV-2 infection in patients younger than 75 years is an independent risk factor for death (odds ratio 2.78, 95% confidence interval 1.44-5.38). INTERPRETATION: Our results show that HA-SARS-CoV-2 infection in younger patients was associated with higher mortality. Future studies need to evaluate relevant patient-centred long-term outcomes in this population.

The PRONTO study: Clinical performance of ID NOW in individuals with compatible SARS-CoV-2 symptoms in walk-in centres-accelerated turnaround time for contact tracing.

BACKGROUND: This PRONTO study investigated the clinical performance of the Abbott ID NOWTM (IDN) COVID-19 diagnostic assay used at point of care and its impact on turnaround time for divulgation of test results. METHODS: Prospective study conducted from December 2020 to February 2021 in acute symptomatic participants presenting in three walk-in centres in the province of Québec. RESULTS: Valid paired samples were obtained from 2,372 participants. A positive result on either the IDN or the standard-of-care nucleic acid amplification test (SOC-NAAT) was obtained in 423 participants (prevalence of 17.8%). Overall sensitivity of IDN and SOC-NAAT were 96.4% (95% CI: 94.2-98.0%) and 99.1% (95% CI: 97.6-99.8), respectively; negative predictive values were 99.2% (95% CI: 98.7-99.6%) and 99.8% (95% CI: 99.5-100%), respectively. Turnaround time for positive results was significantly faster on IDN. CONCLUSION: In our experience, IDN use in symptomatic individuals in walk-in centres is a reliable sensitive alternative to SOC-NAAT without the need for subsequent confirmation of negative results. Such deployment can accelerate contact tracing, reduce the burden on laboratories and increase access to testing.

Community-Based Prevalence Estimates of Chlamydia trachomatis and Neisseria gonorrhoeae Infections Among Gay, Bisexual, and Other Men Who Have Sex With Men in Montréal, Canada.

BACKGROUND: Reported cases of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infections are increasing among Canadian men. Estimates of community-based CT/NG prevalence are lacking among gay, bisexual, and other men who have sex with men (GBM). METHODS: Respondent driven sampling was used to recruit GBM in Montréal, Canada between February 2017 and June 2018. Specimens provided from urogenital, rectal, and pharyngeal sites were analyzed using nucleic acid amplification test to detect CT/NG. Prevalence estimates of CT/NG, overall and by anatomical site were calculated. All estimates are respondent-driven sampling-adjusted. RESULTS: Among 1177 GBM, the prevalence of rectal, urogenital, pharyngeal and overall were respectively 2.4%, 0.4%, 0.4%, and 2.8% for CT infections, and 3.1%, 0.4%, 3.5%, and 5.6% for NG infections. If testing had been limited to the urogenital site, 80% and 94% of CT and NG infections, respectively, would have been missed. CONCLUSIONS: This community-based study among GBM shows that the CT prevalence was about half of that observed for NG. A large part of CT/NG infections involves only the extragenital sites, highlighting the need for systematic multisite screening regardless of symptoms. In the mist of the COVID-19 pandemic and the limited CT/NG screening capacity due to test kits shortage, it might be considered to prioritize rectal and pharyngeal CT/NG testing over urogenital testing in asymptomatic GBM.

Comparison of SARS-CoV-2 detection with the Cobas® 6800/8800 system on gargle samples using two sample processing methods with combined oropharyngeal/nasopharyngeal swab.

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.

Influenza vaccine during the 2019-2020 season and COVID-19 risk: A case-control study in Québec.

BACKGROUND: We carried out a case-control study that examined whether receipt of the inactivated influenza vaccine during the 2019-2020 season impacted on the risk of coronavirus disease 2019 (COVID-19), as there was a concern that the vaccine could be detrimental through viral interference. METHODS: A total of 920 cases with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (diagnosed between March and October 2020) and 2,123 uninfected controls were recruited from those who were born in Québec between 1956 and 1976 and who had received diagnostic services at two hospitals (Montréal and Sherbrooke, Québec). After obtaining consent, a questionnaire was administered by phone. Data were analyzed by logistic regression. RESULTS: Among healthcare workers, inactivated influenza vaccine received during the previous influenza season was not associated with increased COVID-19 risk (AOR: 0.99, 95% CI: 0.69-1.41). Among participants who were not healthcare workers, influenza vaccination was associated with lower odds of COVID-19 (AOR: 0.73, 95% CI 0.56-0.96). CONCLUSION: We found no evidence that seasonal influenza vaccine increased the risk of developing COVID-19.

Natural spring water gargle and direct RT-PCR for the diagnosis of COVID-19 (COVID-SPRING study).

BACKGROUND: Nasopharyngeal swab has long been considered the specimen of choice for the diagnosis of respiratory viral infections, including SARS-CoV-2 infection, but it suffers from several drawbacks: its discomfort limits screening acceptability, and it is vulnerable to shortages in both specialized materials and trained healthcare workers in the context of a pandemic. METHODS: We prospectively compared natural spring water gargle to combined oro-nasopharyngeal swab (ONPS) for the diagnosis of coronavirus disease 2019 (COVID-19) in paired clinical specimens (1005 ONPS and 1005 gargles) collected from 987 unique early symptomatic as well as asymptomatic individuals from the community. RESULTS: Using a direct RT-PCR method with the Allplex™ 2019-nCoV Assay (Seegene), the clinical sensitivity of the gargle was 95.3% (95% confidence interval [CI], 90.2 - 98.3%), similar to the sensitivity of the ONPS (93.8%; 95% CI, 88.2 - 97.3%), despite significantly lower viral RNA concentration in gargles, as reflected by higher cycle threshold values. No single specimen type detected all COVID-19 cases. SARS-CoV-2 RNA was stable in gargles at room temperature for at least 7 days. CONCLUSION: The simplicity of this sampling method coupled with the accessibility of spring water are clear advantages in a pandemic situation where testing frequency, turnaround time and shortage of consumables and trained staff are critical elements.

Does BCG provide long-term protection against SARS-CoV-2 infection? A case-control study in Quebec, Canada.

BACKGROUND: Early in the coronavirus disease 2019 (COVID-19) pandemic, before severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines became available, it was hypothesized that BCG (Bacillus Calmette-Guérin), which stimulates innate immunity, could provide protection against SARS-CoV-2. Numerous ecological studies, plagued by methodological deficiencies, revealed a country-level association between BCG use and lower COVID-19 incidence and mortality. We aimed to determine whether BCG administered in early life decreased the risk of SARS-CoV-2 infection in adulthood and the severity of COVID-19. METHODS: This case-control study was conducted in Quebec, Canada. Cases were patients with a positive SARS-CoV-2 nucleic acid amplification test performed at two hospitals between March-October 2020. Controls were identified among patients with non-COVID-19 samples processed by the same microbiology laboratories during the same period. Enrolment was limited to individuals born in Quebec between 1956 and 1976, whose vaccine status was accessible in a computerized registry of 4.2 million BCG vaccinations. RESULTS: We recruited 920 cases and 2123 controls. Fifty-four percent of cases (n = 424) and 53% of controls (n = 1127) had received BCG during childhood (OR: 1.03; 95% CI: 0.89-1.21), while 12% of cases (n = 114) and 11% of controls (n = 235) had received two or more BCG doses (OR: 1.14; 95% CI: 0.88-1.46). After adjusting for age, sex, material deprivation, recruiting hospital and occupation there was no evidence of protection conferred by BCG against SARS-CoV-2 (AOR: 1.01; 95% CI: 0.84-1.21). Among cases, 77 (8.4%) needed hospitalization and 18 (2.0%) died. The vaccinated were as likely as the unvaccinated to require hospitalization (AOR: 1.01, 95% CI: 0.62-1.67) or to die (AOR: 0.85, 95% CI: 0.32-2.39). CONCLUSIONS: BCG does not provide long-term protection against symptomatic COVID-19 or severe forms of the disease.

Comparison of saliva with oral and nasopharyngeal swabs for SARS-CoV-2 detection on various commercial and laboratory-developed assays.

The accurate laboratory detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a crucial element in the fight against coronavirus disease 2019 (COVID-19). Reverse transcription-polymerase chain reaction testing on combined oral and nasopharyngeal swab (ONPS) suffers from several limitations, including the need for qualified personnel, the discomfort caused by invasive nasopharyngeal sample collection, and the possibility of swab and transport media shortage. Testing on saliva would represent an advancement. The aim of this study was to compare the concordance between saliva samples and ONPS for the detection of SARS-CoV-2 on various commercial and laboratory-developed tests (LDT). Individuals were recruited from eight institutions in Quebec, Canada, if they had SARS-CoV-2 RNA detected on a recently collected ONPS, and accepted to provide another ONPS, paired with saliva. Assays available in the different laboratories (Abbott RealTime SARS-CoV-2, Cobas® SARS-CoV-2, Simplexa™ COVID-19 Direct, Allplex™ 2019-nCoV, RIDA®GENE SARS-CoV-2, and an LDT preceded by three different extraction methods) were used to determine the concordance between saliva and ONPS results. Overall, 320 tests were run from a total of 125 saliva and ONPS sample pairs. All assays yielded similar sensitivity when saliva was compared to ONPS, with the exception of one LDT (67% vs. 93%). The mean difference in cycle threshold (∆C t ) was generally (but not significantly) in favor of the ONPS for all nucleic acid amplification tests. The maximum mean ∆​​​​​C t was 2.0, while individual ∆C t varied importantly from -17.5 to 12.4. Saliva seems to be associated with sensitivity similar to ONPS for the detection of SARS-CoV-2 by various assays.

Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument.

OBJECTIVE: Although several assays have been developed to detect SARS-CoV-2 RNA in clinical specimens, their relative performance is unknown. METHODS: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. RESULTS: The positive and negative agreement between these assays were 99.3 % (95 % CI, 97.3-99.9) and 77.1 % (95 % CI, 67.7-84.4), respectively, for an overall agreement of 93.6 % (95 % CI, 90.7-95.7) beyond random chance (kappa of 0.82, 95 % CI, 0.75-0.85). Of the 22 samples positive by cobas SARS-CoV-2 only, 9 were positive only for ORF-1 gene and had Cycle thresholds (Ct) > 35.1, 8 were positive only for the E gene with Ct > 35.5 and 5 were positive for both targets with Ct > 33.9. Samples positive only with the cobas assay were more often positive with only one gene target (77.3 %) than samples positive in both assays (16.9 %, p < 0.0001). Ct values in the cobas SARS-CoV-2 assay were significantly higher in the 279 samples testing positive in both assays (32.9 %, 95 % CI 32.3-33.6) compared to the 22 samples with discordant results (36.6 %, 95 % CI 36.2-37.1; p = 0.0009). An excellent correlation (r2 = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r2 = 0.82). CONCLUSION: Our study demonstrated an excellent concordance between a LD RT-PCR and the cobas SARS-CoV-2 tests on the 8800 platform.