Herein, we report a case of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and dengue coinfection, presented as a fatal stroke in our hospital, in São José do Rio Preto, São Paulo State, a Brazilian city hyperendemic for dengue viruses and other arthropod‐borne viruses (arboviruses) and currently facing a surge of SARS‐CoV‐2 cases. This case is the first described in the literature and contributes to the better understanding of clinical presentations of two important diseases in a tropical setting.

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.

Background: The emergence of the Brazilian variant of concern, Gamma lineage (P.1), impacted the epidemiological profile of COVID-19 cases due to its higher transmissibility rate and immune evasion ability. Methods: We sequenced 305 SARS-CoV-2 whole-genomes and performed phylogenetic analyses to identify introduction events and the circulating lineages. Additionally, we use epidemiological data of COVID-19 cases, severe cases, and deaths to measure the impact of vaccination coverage and mortality risk. Results: Here we show that Gamma introduction in São José do Rio Preto, São Paulo, Brazil, was followed by the displacement of seven circulating SARS-CoV-2 variants and a rapid increase in prevalence two months after its first detection in January 2021. Moreover, Gamma variant is associated with increased mortality risk and severity of COVID-19 cases in younger age groups, which corresponds to the unvaccinated population at the time. Conclusions: Our findings highlight the beneficial effects of vaccination indicated by a pronounced reduction of severe cases and deaths in immunized individuals, reinforcing the need for rapid and massive vaccination.

The dissemination of the Delta VOC in Brazil is still unclear, despite the frequent reports of isolated cases from different Brazilian states. In this report we characterize the dissemination of the Delta VOC in Brazil and where the introductions of this lineage fall within the global Delta phylogeny. We also examined the mutational profile of the largest clade within the Brazilian Delta VOCs, with a focus on samples which were obtained in the State of Sao Paulo, and especially in the city of Sao Paulo, the largest metropolis of South America, and a national and international transportation hub.

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The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

High frequency screening of populations has been proposed as a strategy in facilitating control of the COVID-19 pandemic. Here we use computational modeling, coupled with clinical data from a rapid antigen test, to predict the impact of frequent rapid testing on COVID-19 spread and outcomes. Using patient nasopharyngeal swab specimens, we demonstrate that the sensitivity and specificity of the rapid antigen test compared to quantitative real-time polymerase chain reaction (qRT-PCR) are 84.7% and 85.7%, respectively; moreover, sensitivity correlates directly with viral load. Based on COVID-19 data from three regions in the United States and Sao Jose do Rio Preto, Brazil, we show that high frequency, strategic population-wide rapid testing, even at varied accuracy levels, diminishes COVID-19 infections, hospitalizations, and deaths at a fraction of the cost of nucleic acid detection via qRT-PCR. We propose large-scale antigen-based surveillance as a viable strategy to control SARS-CoV-2 spread and to enable societal re-opening.

High frequency screening of populations has been proposed as a strategy in facilitating control of the COVID-19 pandemic. We use computational modeling, coupled with clinical data from rapid antigen tests, to predict the impact of frequent viral antigen rapid testing on COVID-19 spread and outcomes. Using patient nasal or nasopharyngeal swab specimens, we demonstrate that the sensitivity/specificity of two rapid antigen tests compared to quantitative real-time polymerase chain reaction (qRT-PCR) are 80.0%/91.1% and 84.7%/85.7%, respectively; moreover, sensitivity correlates directly with viral load. Based on COVID-19 data from three regions in the United States and São José do Rio Preto, Brazil, we show that high frequency, strategic population-wide rapid testing, even at varied accuracy levels, diminishes COVID-19 infections, hospitalizations, and deaths at a fraction of the cost of nucleic acid detection via qRT-PCR. We propose large-scale antigen-based surveillance as a viable strategy to control SARS-CoV-2 spread and to enable societal re-opening.