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In recent years, the SARS-CoV-2 viruses emerged and spread around the world, leaving a large death toll and long-lasting impact on survivors. As of January 2023, Brazil is still among the countries with the highest number of registered deaths. This continental-size and pluralistic country experienced a heterogenous implementation of non-pharmacological and pharmacological interventions which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics across the country. Here we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and its dynamics in distinct epidemiological scenarios in the first two years of the pandemics in the Pernambuco state (Northeast Brazil). We generated a total of 1389 new SARS-CoV-2 genomes from June 2020 to August 2021 covering all major regions of the state. This sampling captured the arrival, communitary transmission and the circulation of the B1.1, B.1.1.28 and B.1.1.33 lineages in the first eight months of the pandemics, the emergence of the former variant of interest P.2 and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma) lineage. Based on the incidence and lineage spread pattern we observed that there was an East-to-West to inner state pattern of transmission which is in agreement with the transmission of more populous metropolitan areas to medium and small size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Nevertheless, inter-state traffic was also another important source of lineage introduction and spread into the state. Our results highlight that the fine grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future non-pharmacological intervention for air-borne transmissible human pathogens.

Introduction: The difficulty in treating Acinetobacter baumannii infections due to its high rate of resistance to antibiotics has led to the study of mechanisms inherent to the pathogen itself that can be used as effective targets in the treatment. Host Factor I Protein (Hfq) is an RNA chaperone generally necessary to assist in the connection between sRNAs and their mRNA target acting in the regulation of different genes, studies carried out in a range of bacterial species have shown that Hfq acts in a pleiotropic manner, contributing to virulence and response stress. Aim: To summarize current knowledge about the role of the Hfq RNA chaperone in the virulence and antibiotic resistance of Acinetobacter baumannii. Outlining: This is an integrative review developed from articles published in any language on Science Direct and PubMed platforms. Data collection and analysis were carried out between the period of April 2020 and February 2021. Results: Hfq shown to play important roles in cell growth, OMVs, metabolism of carbon sources, tolerance to physical and chemical stress, virulence through biofilm formation, fimbriae modulation, among others. Implications: Our work shows data that strengthen the role of Hfq in different aspects of virulence and environmental adaptation, including antimicrobial resistance of this pathogen, warning about the importance of Hfq as a possible future effective target in the treatment of these infections.

Rapid antigen tests play an important role in the monitoring and mitigation of the COVID-19 pandemic, as it provides an easy, fast and efficient diagnosis with minimum infrastructure requirements. However, as new variants of concern continue to emerge, mutations in the virus genome may impair the recognition of the mutated antigen by the tests. Therefore, it is essential to re-assess the test’s sensitivity as the virus mutation profile undergoes significant changes. Here, we prospectively accessed the performance of the DPP® SARS-CoV-2 Antigen test in the context of an omicron-dominant real-life setting. We evaluated 347 unselected individuals (all-comers) from a public testing center in Brazil, performing the rapid antigen test diagnosis at point-of-care with fresh samples. The combinatory result from two distinct RT-qPCR methods was employed as reference and 13 samples with discordant PCR results were excluded. The assessment of the rapid test in 67 PCR-positive and 265 negative samples revealed an overall sensitivity of 80.5%, specificity of 99.2% and positive/negative predictive values higher than 95%. However, we observed that the sensitivity was dependent on the viral load (sensitivity in Ct31 = 47.4%). Furthermore, we were able to confirm that the positive samples evaluated in the study were Omicron (BA.1/BA.1.1) by whole-genome sequencing (n=40) and multiplex RT-qPCR (n=17). Altogether, the data obtained from a real-life prospective cohort supports that the rapid antigen test sensitivity for the Omicron remains high and underscores the reliability of the test for COVID-19 diagnosis in a setting with high disease prevalence and limited PCR testing capability.

The COVID-19 epidemic in Brazil experienced two major lineage replacements until mid-2021. The first was driven by lineage P.2, in late 2020, and the second by lineage Gamma, in early 2021. To understand how these SARS-CoV-2 lineages spread in Brazil, we analyzed 11,724 genomes collected throughout the country between September 2020 and April 2021. Our findings indicate that lineage P.2 probably emerged in July 2020 in the Rio de Janeiro state and Gamma in November 2020 in the Amazonas state. Both states were the main hubs of viral disseminations to other Brazilian locations. We estimate that Gamma was 1.56-3.06 times more transmissible than P.2 in Rio de Janeiro and that the median effective reproductive number (Re) of Gamma varied according to the geographic context (Re = 1.59-3.55). In summary, our findings support that lineage Gamma was more transmissible and spread faster than P.2 in Brazil.