ABSTRACT
COVID-19 has assumed significant and lasting proportions worldwide. Following initial cases in the Western mesoregion, the State of Santa Catarina (SC), southern Brazil, was heavily affected as a whole by the pandemic in early 2021. This study aimed to evaluate the dynamics of the SARS-CoV-2 virus spreading patterns in the SC state through March 2020 to April 2021 using genomic surveillance. During this period, 23 distinct variants, including two VOCs (Beta and Gamma) were identified, among which, the Gamma and related lineages were predominant in the second pandemic wave within SC. However, a regionalization of P.1-like-II in the Western region was observed, concomitant to the increase in cases, mortality, and case fatality rate (CFR) index. This is the first evidence of the regionalization of the SARS-CoV-2 transmission in the and highlight the importance of tracking variants, dispersion and their impact of SARS-CoV-2 on the public health system in Brazilian states.
Subject(s)
COVID-19ABSTRACT
Pool testing has been proposed as an alternative for large-scale SARS-CoV-2 screening. However, dilution factors proportional to the number of pooled samples have been a source of major concern regarding its diagnostic performance. Further, sample pooling can lead to increased laboratory workload and operational complexity. Therefore, pooling strategies that minimize sample dilution, loss of sensitivity, and laboratory overload are needed to allow reliable and large-scale screenings of SARS-CoV-2. Here, we describe a pooling procedure in which nasopharyngeal swabs are pooled together at the time of sample collection (swab pooling), decreasing laboratory manipulation and minimizing dilution of the viral RNA present in the samples. Paired analysis of pooled and individual samples from 613 patients revealed 94 positive individual tests. Having individual testing as a reference, no false-positives or false-negatives were observed for swab pooling. A Bayesian model estimated a sensitivity of 99% (Cr.I. 96.9% to 100%) and a specificity of 99.8% (Cr.I. 99.4% to 100%) for the swab pooling procedure. Data from additional 18,922 patients screened with swab pooling were included for further quantitative analysis. Mean Cq differences between individual and corresponding pool samples ranged from 0.1 Cq (Cr.I. -0.98 to 1.17) to 2.09 Cq (Cr.I. 1.24 to 2.94). Overall, 19,535 asymptomatic and presymptomatic patients were screened using 4,400 RT-qPCR assays, resulting in 246 positive patients (positivity rate 1.26%). This corresponds to an increase of 4.4 times in laboratory capacity and a reduction of 77% in required tests. Finally, these data demonstrate that swab pooling can significantly minimize sample dilution and sensitivity issues commonly seen in its traditional counterpart. Therefore, swab pooling represents a major alternative for reliable and large-scale screening of SARS-CoV-2 in low prevalence populations.
ABSTRACT
We analysed human sewage located in Florianopolis (Santa Catalina, Brazil) from late October until the Brazil lockdown on early March. We detected SARS-CoV-2 in two samples collected independently on 27th November 2019 (5.49{+/-}0.02 log genome copies/L). Subsequent samplings were positive until 4th March 2020 (coinciding with the first COVID-19 case reported in Santa Catalina), with a SARS-CoV-2 RNA increase of one log (6.68{+/-}0.02 log genome copies/L). Our results show that SARS-CoV-2 has been circulating in Brazil since late November 2019, much earlier than the first reported case in the Americas (21st January 2020, USA).