ABSTRACT
SARS-CoV-2 transmission occurs even among fully vaccinated individuals; thus, prompt identification of infected patients is central to control viral circulation. Antigen rapid diagnostic tests (Ag-RDT) are highly specific, but sensitivity is variable. Discordant RT- qPCR vs Ag-RDT results are reported, raising the question of whether negative Ag-RDT in positive RT-qPCR samples could imply the absence of infectious viruses. To study the relationship between a negative Ag-RDT results with virological, molecular, and serological parameters, we selected a cross sectional and a follow-up dataset and analyzed virus culture, subgenomic RNA quantification, and sequencing to determine infectious viruses and mutations. We demonstrated that a positive SARS-CoV-2 Ag-RDT result correlates with the presence of infectious virus in nasopharyngeal samples. A decrease in sgRNA detection together with an expected increase in detectable anti-S and anti-N IgGs was verified in negative Ag-RDT / positive RT-qPCR samples. The data clearly demonstrates the less likelihood of a negative Ag-RDT sample to harbor infectious SARS-CoV-2 and consequently with a lower transmissible potential.
Subject(s)
InfectionsABSTRACT
The Covid-19 pandemic has created an unprecedented need for epidemiological monitoring using diverse strategies. We conducted a project combining prevalence, seroprevalence, and genomic surveillance approaches to describe the initial pandemic stages in Betim City, Brazil. We collected 3239 subjects in a population-based age-, sex- and neighborhood-stratified, household, prospective; cross-sectional study divided into three surveys 21 days apart sampling the same geographical area. In the first survey, overall prevalence (participants positive in serological or molecular tests) reached 0.46% (90% CI 0.12% - 0.80%), followed by 2.69% (90% CI 1.88% - 3.49%) in the second survey and 6.67% (90% CI 5.42% - 7.92%) in the third. The underreporting reached 11, 19.6, and 20.4 times in each survey, respectively. We observed increased odds to test positive in females compared to males (OR 1.88 95% CI 1.25 - 2.82), while the single best predictor for positivity was ageusia/ anosmia (OR 8.12, 95% CI 4.72 - 13.98). Thirty-five SARS-CoV-2 genomes were sequenced, of which 18 were classified as lineage B.1.1.28, while 17 were B.1.1.33. Multiple independent viral introductions were observed. Integration of multiple epidemiological strategies was able to describe Covid-19 dispersion in the city adequately. Presented results have helped local government authorities to guide pandemic management.
Subject(s)
COVID-19 , Olfaction DisordersABSTRACT
Background: The COVID-19 pandemic highly impacted dental healthcare assistance owing to concerns about the risk of transmission by contaminant fluids, droplet formation during dental practice, drastically reducing the number of dental procedures worldwide. This longitudinal study was conducted to monitor SARS-CoV-2 contamination in dental clinics during activities return of students at university.Methods: We evaluated the presence of SARS-CoV-2 RNA by RT-PCR in a dental school clinic environment, on professors, undergraduate dental students, dental assistants, and patients from January 11th to March 12th, 2021 (9 weeks). Serological testing was performed on dental healthcare personnel (DHCP) during the first and last weeks. Additionally, samples with low Ct values were sequenced to identify circulating SARS-CoV-2 variants and possible transmission clusters.Findings: A low number of dental staff (5·8%), patients (0·9%), and environmental sites (0·8%) tested positive for SARS-CoV-2. Most positive cases were asymptomatic to mildly symptomatic, and two asymptomatic DHCP tested positive in longitudinal follow-up RT-PCR test. Previous exposition to COVID-19 were found in 16·2% of the DHCP that showed IgM or IgG antibodies against SARS-CoV-2, and 1/3 of them had undetected antibodies in the last week. Variant Zeta (P.2) were detected. No cross-infection was observed among the participants.Interpretation: Our study suggests that dental practice can be executed safely when control measures and biosafety protocols are applied adequately. DHCP and patient testing, telemonitoring, proper use of personal protection equipment, and surface sanitisation are essential to avoid SARS-CoV-2 cross-infection in dental practice.Funding Information: UFMG/RTR/PRPq, FAPEMIG, CNPq, CAPES/MEC, FINEP, and Rede Corona-ômica BR MCTI/FINEP affiliated to RedeVírus/MCTI.Declaration of Interests: All authors declare to have no conflict of interests.Ethics Approval Statement: The present study was approved by the Ethics Committee of Universidade Federal de Minas Gerais (UFMG) (Protocol nº31041720.3.0000.5149) (https://plataformabrasil.saude.gov.br/login.jsf). All participants enrolled in this study were volunteers, and their samples and clinical data were collected only via signed consent forms.
Subject(s)
COVID-19ABSTRACT
The emergence and widespread circulation of SARS-CoV-2 variants of concern (VOC) or interest (VOI) imposes an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates this variant has circulated locally since the first weeks of 2021 and only seven weeks were necessary for it to achieve a frequency above 70%, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates VOC Gamma spread throughout Brazil between December 2020 and January 2021, and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of RT-qPCR cycle threshold (Ct) values provide further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95% CI = 2.0 - 3.4). This analysis corroborates the previously proposed mechanistic basis for this variant enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.
ABSTRACT
Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Due to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus transmission and epidemic spread remain challenging. We investigate the impact of NPIs in Brazil using epidemiological, mobility and genomic data. Mobility-driven transmission models for Sao Paulo and Rio de Janeiro cities show that the reproduction number (Rt) reached below 1 following NPIs but slowly increased to values between 1 to 1.3 (1.0 - -1.6). Genome sequencing of 427 new genomes and analysis of a geographically representative genomic dataset from 21 of the 27 Brazilian states identified >100 international introductions of SARS-CoV-2 in Brazil. We estimate that three clades introduced from Europe emerged between 22 and 27 February 2020, and were already well-established before the implementation of NPIs and travel bans. During this first phase of the epidemic establishment of SARS-CoV-2 in Brazil, we find that the virus spread mostly locally and within-state borders. Despite sharp decreases in national air travel during this period, we detected a 25% increase in the average distance travelled by air passengers during this time period. This coincided with the spread of SARS-CoV-2 from large urban centers to the rest of the country. In conclusion, our results shed light on the role of large and highly connected populated centres in the rapid ignition and establishment of SARS-CoV-2, and provide evidence that current interventions remain insufficient to keep virus transmission under control in Brazil.