Oral saliva swab reverse transcription PCR for Covid-19 in the paediatric population.

OBJECTIVES: To evaluate the performance of oral saliva swab (OSS) reverse transcription PCR (RT-PCR) compared with RT-PCR and antigen rapid diagnostic test (Ag-RDT) on nasopharyngeal swabs (NPS) for SARS-CoV-2 in children. DESIGN: Cross-sectional multicentre diagnostic study. SETTING: Study nested in a prospective, observational cohort (EPICO-AEP) performed between February and March 2021 including 10 hospitals in Spain. PATIENTS: Children from 0 to 18 years with symptoms compatible with Covid-19 of ≤5 days of duration were included. Two NPS samples (Ag-RDT and RT-PCR) and one OSS sample for RT-PCR were collected. MAIN OUTCOME: Performance of Ag-RDT and RT-PCR on NPS and RT-PCR on OSS sample for SARS-CoV-2. RESULTS: 1174 children were included, aged 3.8 years (IQR 1.7-9.0); 73/1174 (6.2%) patients tested positive by at least one of the techniques. Sensitivity and specificity of OSS RT-PCR were 72.1% (95% CI 59.7 to 81.9) and 99.6% (95% CI 99 to 99.9), respectively, versus 61.8% (95% CI 49.1 to 73) and 99.9% (95% CI 99.4 to 100) for the Ag-RDT. Kappa index was 0.79 (95% CI 0.72 to 0.88) for OSS RT-PCR and 0.74 (95% CI 0.65 to 0.84) for Ag-RDT versus NPS RT-PCR. CONCLUSIONS: RT-PCR on the OSS sample is an accurate option for SARS-CoV-2 testing in children. A less intrusive technique for younger patients, who usually are tested frequently, might increase the number of patients tested.

SARS-CoV-2 surveillance strategy in essential workers of the Madrid City Council during the first epidemic wave in Spain, March-July 2020.

OBJECTIVES: To study prevalence of infection in essential workers of Madrid City Council by occupation, related characteristics, use of protective devices, risk perception, and main concerns about COVID-19 during lockdown. METHODS: A total of 30 231 workers were PCR tested for SARS-CoV-2 infection. Information was collected on COVID-19-related symptoms, risk factors, preventive equipment, and risk perception. The crude prevalence was calculated for infection, use of protective devices, perceived risk and main concerns. Additionally, adjusted prevalence and prevalence ratios (PR) were estimated for these variables using logistic regression models with age, gender, occupation, epidemiological week and laboratory as confounding factors. RESULTS: Overall prevalence of infection was 3.2% (95% CI 3.0% to 3.4%), being higher among policemen (4.4%) and bus drivers (4.2%), but lower among emergency healthcare personnel, firefighters, food market workers and burial services (<2%). Lower excess risk was observed in workers reporting occupational contact with COVID-19 cases only (PR=1.42; 95% CI 1.18 to 1.71) compared with household exposure only (PR=2.75; 95% CI 2.32 to 3.25). Infection was more frequent in symptomatic workers (PR=1.28; 95% CI 1.11 to 1.48), although 42% of detected infections were asymptomatic. Use of facial masks (78.7%) and disinfectants (86.3%) was common and associated with lower infection prevalence (PRmasks=0.68; 95% CI 0.58 to 0.79; PRdisinfectants=0.75; 95% CI 0.61 to 0.91). Over 50% of workers felt being at high risk of infection and worried about infecting others, yet only 2% considered quitting their work. CONCLUSIONS: This surveillance system allowed for detecting and isolating SARS-CoV-2 cases among essential workers, identifying characteristics related to infection and use of protective devices, and revealing specific needs for work-safety information and psychological support.

The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (Re < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants.

Sequencing of SARS-CoV-2 genome using different nanopore chemistries.

Nanopore sequencing has emerged as a rapid and cost-efficient tool for diagnostic and epidemiological surveillance of SARS-CoV-2 during the COVID-19 pandemic. This study compared the results from sequencing the SARS-CoV-2 genome using R9 vs R10 flow cells and a Rapid Barcoding Kit (RBK) vs a Ligation Sequencing Kit (LSK). The R9 chemistry provided a lower error rate (3.5%) than R10 chemistry (7%). The SARS-CoV-2 genome includes few homopolymeric regions. Longest homopolymers were composed of 7 (TTTTTTT) and 6 (AAAAAA) nucleotides. The R10 chemistry resulted in a lower rate of deletions in thymine and adenine homopolymeric regions than the R9, at the expenses of a larger rate (~10%) of mismatches in these regions. The LSK had a larger yield than the RBK, and provided longer reads than the RBK. It also resulted in a larger percentage of aligned reads (99 vs 93%) and also in a complete consensus genome. The results from this study suggest that the LSK preparation library provided longer DNA fragments which contributed to a better assembly of the SARS-CoV-2, despite an impaired detection of variants in a R10 flow cell. Nanopore sequencing could be used in epidemiological surveillance of SARS-CoV-2. KEY POINTS: • Sequencing SARS-CoV-2 genome is of great importance for the pandemic surveillance. • Nanopore offers a low cost and accurate method to sequence SARS-CoV-2 genome. • Ligation sequencing is preferred rather than the rapid kit using transposases.