Molecular Epidemiology of Mayaro Virus among Febrile Patients, Roraima State, Brazil, 2018-2021.

We detected Mayaro virus (MAYV) in 3.4% (28/822) of febrile patients tested during 2018-2021 from Roraima State, Brazil. We also isolated MAYV strains and confirmed that these cases were caused by genotype D. Improved surveillance is needed to better determine the burden of MAYV in the Amazon Region.

Predicting Exacerbations in Alpha-1 Antitrypsin Deficiency Using Clinical and Pulmonary Function Tests: Portuguese EARCO Registry.

INTRODUCTION: Exacerbations are common in individuals with alpha-1 antitrypsin deficiency (AATD)-related lung disease. This study intended to identify independent predictive factors for exacerbations in AATD using the Portuguese European Alpha-1 Research Collaboration (EARCO) registry. METHODS: This study includes patients from the Portuguese EARCO registry, a prospective multicenter cohort (NCT04180319). From October 2020 to April 2023, this registry enrolled 137 patients, 14 of whom were excluded for analysis for either missing 12 months of follow-up or baseline pulmonary function. RESULTS: Among the 123 AATD patients, 27 (22.0%) had at least one exacerbation in the last 12 months of follow-up. Patients with Pi*ZZ phenotype were three times more likely than the rest of the population to experience any exacerbation (32.7 vs. 14.1%, p = 0.014; OR 3.0). BODE index was significantly higher in exacerbators than in non-exacerbators (3.9 ± 2.4 vs. 1.3 ± 1.2; p < 0.001), including on multivariate analysis (p = 0.002). Similar results were found for BODEx (multivariate p < 0.001). DLCO was the only functional parameter independently associated with exacerbations (p = 0.024). CONCLUSIONS: DLCO, BODE, and BODEx were independent predictors of exacerbations at 12 months in AATD patients. Understanding these risk factors can aid decision-making on AATD-related lung disease management and improve patient outcomes.

A Novel Biosurfactant-Based Oil Spill Response Dispersant for Efficient Application under Temperate and Arctic Conditions.

Synthetic oil spill dispersants have become essential in offshore oil spill response strategies. However, their use raises significant concerns regarding toxicity to phyto- and zooplankton and other marine organisms, especially in isolated and vulnerable areas such as the Arctic and shorelines. Sustainable alternatives may be developed by replacing the major active components of commercial dispersants with their natural counterparts. During this study, interfacial properties of different types of glycolipid-based biosurfactants (rhamnolipids, mannosylerythritol lipids, and trehalose lipids) were explored in a crude oil-seawater system. The best-performing biosurfactant was further mixed with different nontoxic components of Corexit 9500A, and the interfacial properties of the most promising dispersant blend were further explored with various types of crude oils, weathered oil, bunker, and diesel fuel in natural seawater. Our findings indicate that the most efficient dispersant formulation was achieved when mannosylerythritol lipids (MELs) were mixed with Tween 80 (T). The MELs-T dispersant blend significantly reduced the interfacial tension (IFT) of various crude oils in seawater with results comparable to those obtained with Corexit 9500A. Importantly, no leaching or desorption of MELs-T components from the crude oil-water interface was observed. Furthermore, for weathered and more viscous asphaltenic bunker fuel oil, IFT results with the MELs-T dispersant blend surpassed those obtained with Corexit 9500A. This dispersant blend also demonstrated effectiveness at different dosages (dispersant-to-oil ratio (DOR)) and under various temperature conditions. The efficacy of the MELs-T dispersant was further confirmed by standard baffled flask tests (BFTs) and Mackay-Nadeau-Steelman (MNS) tests. Overall, our study provides promising data for the development of effective biobased dispersants, particularly in the context of petroleum exploitation in subsea resources and transportation in the Arctic.

The Looming Threat of Dengue Fever: The Africa Context.

In Africa, compared to 2019, dengue infections have surged ninefold by December 2023, with over 270 000 cases and 753 deaths reported across 18 African Union (AU) Member States. This commentary synthesises the context of dengue outbreaks in Africa and provides recommendations for sustainable control. In 2023, 18 African Union Member States reported outbreaks of dengue, among which seven had ongoing armed conflicts. These countries were amongst the top 15 African countries contributing to the most displaced persons on the continent and accounted for 98% of all dengue cases reported in the continent in 2023. Climate change remains an important driver, both through the displacement of people and global warming. The continent continues to face several challenges in detection, reporting and management, such as the lack of local laboratory capacity, misclassification of dengue cases and lack of medical countermeasures. Solutions targeting the strengthening of cross-border surveillance and early warning systems using a multisectoral one-health approach, local research and development for therapeutics and diagnostics and community engagement empowering communities to protect themselves and understand the gravity of the threat could help curb the spread of the disease in Africa.

Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes.

The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.

A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva.

The gold standard for coronavirus disease 2019 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through reverse transcription-polymerase chain reaction (RT-PCR) with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection made it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from saliva samples or RNA isolated from nasopharyngeal (NP) swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost, and in some cases, the saliva test outperformed NP rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics.

SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient.

This study aimed to provide further insight into the evolutionary dynamics of SARS-CoV-2 by analyzing the case of a 40-year-old man who had previously undergone autologous hematopoietic stem cell transplantation due to a diffuse large B-cell lymphoma. He developed a persistent SARS-CoV-2 infection lasting at least 218 days and did not manifest a humoral immune response to the virus during this follow-up period. Whole-genome sequencing and viral cultures confirmed a persistent infection with a replication-positive virus that had undergone genetic variation for at least 196 days after symptom onset.

Chikungunya: a decade of burden in the Americas.

In the Americas, one decade following its emergence in 2013, chikungunya virus (CHIKV) continues to spread and cause epidemics across the region. To date, 3.7 million suspected and laboratory-confirmed chikungunya cases have been reported in 50 countries or territories in the Americas. Here, we outline the current status and epidemiological aspects of chikungunya in the Americas and discuss prospects for future research and public health strategies to combat CHIKV in the region.

Clinical and epidemiological characteristics of Madariaga and Venezuelan equine encephalitis virus infections.

Madariaga virus (MADV) and Venezuelan equine encephalitis virus (VEEV) are emerging arboviruses affecting rural and remote areas of Latin America. However, there are limited clinical and epidemiological reports available, and outbreaks are occurring at an increasing frequency. We addressed this gap by analyzing all the available clinical and epidemiological data of MADV and VEEV infections recorded since 1961 in Panama. A total of 168 of human alphavirus encephalitis cases were detected in Panama from 1961 to 2023. Here we describe the clinical signs and symptoms and epidemiological characteristics of these cases, and also explored signs and symptoms as potential predictors of encephalitic alphavirus infection when compared to those of other arbovirus infections occurring in the region. Our results highlight the challenges clinical diagnosis of alphavirus disease in endemic regions with overlapping circulation of multiple arboviruses.

Human movement and environmental barriers shape the emergence of dengue.

Understanding how emerging infectious diseases spread within and between countries is essential to contain future pandemics. Spread to new areas requires connectivity between one or more sources and a suitable local environment, but how these two factors interact at different stages of disease emergence remains largely unknown. Further, no analytical framework exists to examine their roles. Here we develop a dynamic modelling approach for infectious diseases that explicitly models both connectivity via human movement and environmental suitability interactions. We apply it to better understand recently observed (1995-2019) patterns as well as predict past unobserved (1983-2000) and future (2020-2039) spread of dengue in Mexico and Brazil. We find that these models can accurately reconstruct long-term spread pathways, determine historical origins, and identify specific routes of invasion. We find early dengue invasion is more heavily influenced by environmental factors, resulting in patchy non-contiguous spread, while short and long-distance connectivity becomes more important in later stages. Our results have immediate practical applications for forecasting and containing the spread of dengue and emergence of new serotypes. Given current and future trends in human mobility, climate, and zoonotic spillover, understanding the interplay between connectivity and environmental suitability will be increasingly necessary to contain emerging and re-emerging pathogens.

Reemergence of Oropouche virus between 2023 and 2024 in Brazil.

Background: Oropouche virus (OROV; species Orthobunyavirus oropoucheense) is an arthropod-borne virus that has caused outbreaks of Oropouche fever in Central and South America since the 1950s. This study investigates virological factors contributing to the reemergence of Oropouche fever in Brazil between 2023 and 2024. Methods: In this study, we combined OROV genomic, molecular, and serological data from Brazil from 1 January 2015 to 29 June 2024, along with in vitro and in vivo characterization. Molecular screening data included 93 patients with febrile illness between January 2023 and February 2024 from the Amazonas State. Genomic data comprised two genomic OROV sequences from patients. Serological data were obtained from neutralizing antibody tests comparing the prototype OROV strain BeAn 19991 and the 2024 epidemic strain. Epidemiological data included aggregated cases reported to the Brazilian Ministry of Health from 1 January 2014 to 29 June 2024. Findings: In 2024, autochthonous OROV infections were detected in previously non-endemic areas across all five Brazilian regions. Cases were reported in 19 of 27 federal units, with 83.2% (6,895 of 8,284) of infections in Northern Brazil and a nearly 200-fold increase in incidence compared to reported cases over the last decade. We detected OROV RNA in 10.8% (10 of 93) of patients with febrile illness between December 2023 and May 2024 in Amazonas. We demonstrate that the 2023-2024 epidemic was caused by a novel OROV reassortant that replicated approximately 100-fold higher titers in mammalian cells compared to the prototype strain. The 2023-2024 OROV reassortant displayed plaques earlier than the prototype, produced 1.7 times more plaques, and plaque sizes were 2.5 larger compared to the prototype. Furthermore, serum collected in 2016 from previously OROV-infected individuals showed at least a 32-fold reduction in neutralizing capacity against the reassortment strain compared to the prototype. Interpretation: These findings provide a comprehensive assessment of Oropouche fever in Brazil and contribute to a better understanding of the 2023-2024 OROV reemergence. The recent increased incidence may be related to a higher replication efficiency of a new reassortant virus that also evades previous immunity.

A new lineage nomenclature to aid genomic surveillance of dengue virus.

Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here we propose adding two sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present an assignment tool to show that the proposed lineages are useful for regional, national and sub-national discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.

Lessons from a Multilaboratorial Task Force for Diagnosis of a Fatal Toxoplasmosis Outbreak in Captive Primates in Brazil.

Toxoplasmosis is an important zoonotic disease caused by the parasite Toxoplasma gondii and is especially fatal for neotropical primates. In Brazil, the Ministry of Health is responsible for national epizootic surveillance, but some diseases are still neglected. Here, we present an integrated investigation of an outbreak that occurred during the first year of the COVID-19 pandemic among eleven neotropical primates housed at a primatology center in Brazil. After presenting non-specific clinical signs, all animals died within four days. A wide range of pathogens were evaluated, and we successfully identified T. gondii as the causative agent within four days after necropsies. The liver was the most affected organ, presenting hemorrhage and hepatocellular necrosis. Tachyzoites and bradyzoite cysts were observed in histological examinations and immunohistochemistry in different organs; in addition, parasitic DNA was detected through PCR in blood samples from all specimens evaluated. A high prevalence of Escherichia coli was also observed, indicating sepsis. This case highlights some of the obstacles faced by the current Brazilian surveillance system. A diagnosis was obtained through the integrated action of researchers since investigation for toxoplasmosis is currently absent in national guidelines. An interdisciplinary investigation could be a possible model for future epizootic investigations in animals.

SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient

ABSTRACT This study aimed to provide further insight into the evolutionary dynamics of SARS-CoV-2 by analyzing the case of a 40-year-old man who had previously undergone autologous hematopoietic stem cell transplantation due to a diffuse large B-cell lymphoma. He developed a persistent SARS-CoV-2 infection lasting at least 218 days and did not manifest a humoral immune response to the virus during this follow-up period. Whole-genome sequencing and viral cultures confirmed a persistent infection with a replication-positive virus that had undergone genetic variation for at least 196 days after symptom onset.

Role of the one-minute sit-to-stand test in the diagnosis of post COVID-19 condition: a prospective cohort study / Papel do teste de se sentar e levantar durante um minuto no diagnóstico de síndrome pós-COVID-19: estudo prospectivo de coorte

ABSTRACT Objective: To analyze the relationship between one-minute sit-to-stand test (1MSTST) parameters and a diagnosis of post COVID-19 condition in a cohort of patients who previously had COVID-19. Methods: This was a prospective cohort study of patients with post COVID-19 condition referred for body plethysmography at a tertiary university hospital. Post COVID-19 condition was defined in accordance with the current WHO criteria. Results: Fifty-three patients were analyzed. Of those, 25 (47.2%) met the clinical criteria for post COVID-19 condition. HR was lower in the patients with post COVID-19 condition than in those without it at 30 s after initiation of the 1MSTST (86.2 ± 14.3 bpm vs. 101.2 ± 14.7 bpm; p < 0.001) and at the end of the test (94.4 ± 18.2 bpm vs. 117.3 ± 15.3 bpm; p < 0.001). The ratio between HR at the end of the 1MSTST and age-predicted maximal HR (HRend/HRmax) was lower in the group of patients with post COVID-19 condition (p < 0.001). An HRend/HRmax of < 62.65% showed a sensitivity of 78.6% and a specificity of 82.0% for post COVID-19 condition. Mean SpO2 at the end of the 1MSTST was lower in the patients with post COVID-19 condition than in those without it (94.9 ± 3.6% vs. 96.8 ± 2.4%; p = 0.030). The former group of patients did fewer repetitions on the 1MSTST than did the latter (p = 0.020). Conclusions: Lower SpO2 and HR at the end of the 1MSTST, as well as lower HR at 30 s after initiation of the test, were associated with post COVID-19 condition. In the appropriate clinical setting, an HRend/HRmax of < 62.65% should raise awareness for the possibility of post COVID-19 condition.

RESUMO Objetivo: Analisar a relação entre parâmetros do teste de se sentar e levantar durante um minuto (TSL1) e o diagnóstico de síndrome pós-COVID-19 em uma coorte de pacientes que anteriormente apresentaram COVID-19. Métodos: Estudo prospectivo de coorte de pacientes com síndrome pós-COVID-19 encaminhados para realizar pletismografia corporal em um hospital universitário terciário. A síndrome pós-COVID-19 foi definida conforme os critérios atuais da OMS. Resultados: Foram analisados 53 pacientes. Destes, 25 (47,2%) preencheram os critérios clínicos de síndrome pós-COVID-19. A FC foi menor nos pacientes com síndrome pós-COVID-19 do que naqueles sem a síndrome 30 s após o início do TSL1 (86,2 ± 14,3 bpm vs. 101,2 ± 14,7 bpm; p < 0,001) e no fim do teste (94,4 ± 18,2 bpm vs. 117,3 ± 15,3 bpm; p < 0,001). A relação entre a FC no fim do TSL1 e a FC máxima prevista para a idade (FCfim/FCmáx) foi menor nos pacientes com síndrome pós-COVID-19 (p < 0,001). A relação FCfim/FCmáx < 62,65% apresentou sensibilidade de 78,6% e especificidade de 82,0% para síndrome pós-COVID-19. A média da SpO2 no fim do TSL1 foi menor nos pacientes com síndrome pós-COVID-19 do que naqueles sem a síndrome (94,9 ± 3,6% vs. 96,8 ± 2,4%; p = 0,030). Os pacientes com síndrome pós-COVID-19 realizaram menos repetições durante o TSL1 do que os sem a síndrome (p = 0,020). Conclusões: SpO2 e FC mais baixas no fim do TSL1 e FC mais baixa 30 s após o início do teste apresentaram relação com síndrome pós-COVID-19. No contexto clínico apropriado, a relação FCfim/FCmáx < 62,65% deve alertar para a possibilidade de síndrome pós-COVID-19.

Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022

ABSTRACT Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.

Genomics and epidemiology of the P 1 SARS-CoV-2 lineage in Manaus, Brazil

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 ­ 2018

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV

Importation and early local transmission of COVID-19 in Brazil, 2020

We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil. (AU)