Rapid increase in SARS-CoV-2 seroprevalence during the emergence of Omicron variant, Finland

ObjectivesThe aim of this study was to assess changes in exposure and prevalence of SARS-CoV-2 infection during the first months of emergence of Omicron variant in the Greater Helsinki area, Finland. MethodsA prospective seroepidemiological survey of SARS-CoV-2 was conducted on 1,600 serum specimens sent to Helsinki University Hospital Laboratory (HUSLAB) for HIV serology between 15 November 2021 and 6 March 2022 (calendar weeks 46/2021 - 9/2022). For each calendar week, 100 serum specimens were randomly selected and analysed for SARS-CoV-2 IgG antibodies against nucleocapsid (N) and spike 1 (S1) protein with Abbott SARS-CoV-2 IgG (N protein) and SARS-CoV-2 IgG II Quant (S protein) tests, respectively. ResultsThe prevalence of N antibodies increased from 5.2% (weeks 46-50/2021) to 28.2% (weeks 5-9/2022) during the study period. The proportion of seronegative samples as well as anti-N negative, anti-S1 positive samples decreased correspondingly from 11.6% to 3.8%, and 84.2% to 68.2%, respectively. Anti-N positive samples that were anti-S1 negative only began to appear as of week 2/2022. ConclusionsA rapid increase in the N antibody prevalence was observed over the study period, suggesting a high transmission rate. A substantial proportion of COVID-19 cases remained undiagnosed during the emergence of Omicron variant in the Greater Helsinki Area, Finland.

Detection of SARS-CoV-2 nucleocapsid antigen from serum can aid in timing of COVID-19 infection

SARS-CoV-2 RNA can be detected in respiratory samples for weeks or even months after onset of COVID-19 disease. Therefore, one of the diagnostic challenges of PCR positive cases is differentiating between acute COVID-19 disease and convalescent phase. Recently, the presence of SARS-CoV-2 nucleocapsid antigen in serum samples of COVID-19 patients was published [Le Hingrat et al. Detection of SARS-CoV-2 N-antigen in blood during acute COVID-19 provides a sensitive new marker and new testing alternatives, Clinical Microbiology and Infection, 2020]. Our study aimed to characterize the analytical specificity and sensitivity of an enzyme-linked immunosorbent assay (Salocor SARS-CoV-2 Antigen Quantitative Assay Kit(C) (Salofa Ltd, Salo, Finland)) for the detection of SARS-CoV-2 antigen in serum, and to characterize the kinetics of antigenemia. The evaluation material included a negative serum panel of 155 samples, and 126 serum samples from patients with PCR-confirmed COVID-19. The specificity of the Salocor SARS-CoV-2 serum N antigen test was 98.0%. In comparison with simultaneous positive PCR from upper respiratory tract (URT) specimens, the test sensitivity was 91.7%. In a serum panel in which the earliest serum sample was collected two days before the collection of positive URT specimen, and the latest 48 days after (median 1 day post URT sample collection), the serum N antigen test sensitivity was 94% within 14 days post onset of symptoms. The antigenemia resolved approximately two weeks after the onset of disease and diagnostic PCR. The combination of simultaneous SARS-CoV-2 antigen and antibody testing appeared to provide useful information for the timing of COVID-19. Our results suggest that SARS-CoV-2 N-antigenemia may be used as a diagnostic marker in acute COVID-19.

Real-life clinical sensitivity of SARS-CoV-2 RT-PCR test in symptomatic patients

ImportanceUnderstanding the false negative rates of SARS-CoV-2 RT-PCR testing is pivotal for the management of the COVID-19 pandemic and it has practical implications for patient management in healthcare facilities. ObjectiveTo determine the real-life clinical sensitivity of SARS-CoV-2 RT-PCR testing. DesignA retrospective study on case series from 4 March - 15 April 2020. SettingA population-based study conducted in primary and tertiary care in the Helsinki Capital Region, Finland. ParticipantsAdults who were clinically suspected of SARS-CoV-2 infection and underwent SARS-CoV-2 RT-PCR testing, and who had sufficient data for grading of clinical suspicion of COVID-19 in their medical records were eligible. All 1,194 inpatients admitted to COVID-19 cohort wards during the study period were included. The outpatient cohort of 1,814 individuals was sampled from epidemiological line lists by systematic quasi-random sampling. Altogether 83 eligible outpatients (4.6%) and 3 inpatients (0.3%) were excluded due to insufficient data for grading of clinical suspicion. ExposuresHigh clinical suspicion for COVID-19 was used as the reference standard for the RT-PCR test. Patients were considered to have high clinical suspicion of COVID-19 if the physician in charge recorded the suspicion on clinical grounds, or the patient fulfilled specifically defined clinical and exposure criteria. Main measuresSensitivity of SARS-CoV-2 RT-PCR by using manually curated clinical characteristics as the gold standard. ResultsThe study population included 1,814 outpatients (mean [SD] age, 45.4 [17.2] years; 69.1% women) and 1,194 inpatients (mean [SD] age, 63.2 [18.3] years; 45.2% women). The sensitivity (95% CI) for laboratory confirmed cases, i.e. repeatedly tested patients were as follows: 85.7% (81.5-89.1%) inpatients; 95.5% (92.2-97.5%) outpatients, 89.9% (88.2-92.1%) all. When also patients that were graded as high suspicion but never tested positive were included in the denominator, the following sensitivity values (95% CI) were observed: 67.5% (62.9-71.9%) inpatients; 34.9% (31.4-38.5%) outpatients; 47.3% (44.4-50.3%) all. Conclusions and relevanceThe clinical sensitivity of SARS-CoV-2 RT-PCR testing was only moderate at best. The relatively high false negative rates of SARS-CoV-2 RT-PCR testing need to be accounted for in clinical decision making, epidemiological interpretations and when using RT-PCR as a reference for other tests. Key PointsO_ST_ABSQuestionC_ST_ABSWhat is the clinical sensitivity of SARS-CoV-2 RT-PCR test? FindingsIn this population-based retrospective study on medical records of 1,814 outpatients and 1,194 inpatients, the clinical sensitivity of SARS-CoV-2 RT-PCR was 47.3-89.9%. MeaningThe false negative rates of SARS-CoV-2 RT-PCR testing need to be accounted for in clinical decision making, epidemiological interpretations and when using RT-PCR as a reference for other tests.

SARS-CoV-2 sample-to-answer nucleic acid testing in a tertiary care emergency department: evaluation and utility

Rapid sample-to-answer tests for detection of SARS-CoV-2 are emerging and data on their relative performance is urgently needed. We evaluated the analytical performance of two rapid nucleic acid tests, Cepheid Xpert(R) Xpress SARS-CoV-2 and Mobidiag Novodiag(R) Covid-19, in comparison to a combination reference of three large-scale PCR tests. Moreover, utility of the Novodiag(R) test in tertiary care emergency departments was assessed. In the preliminary evaluation, analysis of 90 respiratory samples resulted in 100% specificity and sensitivity for Xpert(R), whereas analysis of 107 samples resulted in 93.4% sensitivity and 100% specificity for Novodiag(R). Rapid SARS-CoV-2 testing with Novodiag(R) was made available for four tertiary care emergency departments in Helsinki, Finland between 18 and 31 May, coinciding with a rapidly declining epidemic phase. Altogether 361 respiratory specimens, together with relevant clinical data, were analyzed with Novodiag(R) and reference tests: 355/361 of the specimens were negative with both methods, and 1/361 was positive in Novodiag(R) and negative by the reference method. Of the 5 remaining specimens, two were negative with Novodiag(R), but positive with the reference method with late Ct values. On average, a test result using Novodiag(R) was available nearly 8 hours earlier than that obtained with the large-scale PCR tests. While the performance of novel sample-to-answer PCR tests need to be carefully evaluated, they may provide timely and reliable results in detection of SARS-CoV-2 and thus facilitate patient management including effective cohorting.

Comparison of two commercial platforms and a laboratory developed test for detection of SARS-CoV-2 RNA

Mitigation of the ongoing COVID-19 pandemic requires reliable and accessible laboratory diagnostic services. We evaluated the performance of one LDT and two commercial tests, cobas(R) SARS-CoV-2 (Roche) and Amplidiag(R) COVID-19 (Mobidiag), for the detection of SARS-CoV-2 RNA in respiratory specimens. 183 specimens collected from suspected COVID-19 patients were studied with all three methods to compare their performance. In relation to the reference standard, which was established as the result obtained by two of the three studied methods, the positive percent agreement (PPA) was highest for cobas(R) test (100%), followed by Amplidiag(R) test and the LDT (98.9%). The negative percent agreement (NPA) was lowest for cobas(R) test (89.4%), followed by Amplidiag(R) test (98.8%) and the highest value was obtained for LDT (100%). The dilution series conducted for specimens, however, suggests significantly higher sensitivity for the cobas(R) assay in comparison with the other two assays and the low NPA value may be due to the same reason. In general, all tested assays performed adequately. Both the time from sample to result and hands-on time per sample were shortest for cobas(R) test. Clinical laboratories need to be prepared for uninterrupted high-throughput testing during the coming months in mitigation of the pandemic. To secure that, it is of critical importance for clinical laboratories to maintain several simultaneous platforms in their SARS-CoV-2 nucleic acid testing.

Laboratory-based surveillance of COVID-19 in the Greater Helsinki area, Finland, February-June 2020

Laboratory registry data (80,791 specimens, 70,517 individuals) was used to characterise age- and sex-specific SARS-CoV-2 RT-PCR sampling frequency and positivity rate, and laboratory capacity building in Greater Helsinki, Finland during February-June 2020. While the number of positive cases was similar in males and females, the positivity rate was significantly higher in males. The highest incidence/100,000 was observed in those aged [≥]80 years. The proportion of young adults in positive cases increased in late May 2020.

Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation

There is an urgent need for reliable high-throughput serological assays for the management of the ongoing COVID-19 pandemic. Preferably, the performance of serological tests for a novel virus should be determined with clinical specimens against a gold standard, i.e. virus neutralisation. We evaluated specificity and sensitivity of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison(R) SARS-CoV-2 S1/S2 IgG (research use only), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] in comparison with a microneutralisation test (MNT). Two specimen panels from serum samples sent to Helsinki University Hospital Laboratory (HUSLAB) were compiled: the patient panel included sera from PCR confirmed COVID-19 patients, and the negative panel included sera sent for screening of autoimmune diseases and respiratory virus antibodies in 2018 and 2019. The MNT was carried out for all COVID-19 samples (70 serum samples, 62 individuals) and for 53 samples from the negative panel. Forty-one out of 62 COVID-19 patients showed neutralising antibodies with median of 11 days (range 3-51) after onset of symptoms. The specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARSCoV-2 IgM). This study shows variable performance values. Laboratories should carefully consider their testing process, such as a two-tier approach, in order to optimize the overall performance of SARS-CoV-2 serodiagnostics.