Time to harmonize dengue nomenclature and classification

Dengue virus (DENV) is estimated to cause 390 million infections per year worldwide. A quarter of these infections manifest clinically and are associated with a morbidity and mortality that put a significant burden on the affected regions. Reports of increased frequency, intensity, and extended geographical range of outbreaks highlight the virus's ongoing global spread. Persistent transmission in endemic areas and the emergence in territories formerly devoid of transmission have shaped DENV's current genetic diversity and divergence. This genetic layout is hierarchically organized in serotypes, genotypes, and sub-genotypic clades. While serotypes are well defined, the genotype nomenclature and classification system lack consistency, which complicates a broader analysis of their clinical and epidemiological characteristics. We identify five key challenges: (1) Currently, there is no formal definition of a DENV genotype; (2) Two different nomenclature systems are used in parallel, which causes significant confusion; (3) A standardized classification procedure is lacking so far; (4) No formal definition of sub-genotypic clades is in place; (5) There is no consensus on how to report antigenic diversity. Therefore, we believe that the time is right to re-evaluate DENV genetic diversity in an essential effort to provide harmonization across DENV studies.publishersversionpublishe

Digitalization by means of a prototyping process : the case of a Brazilian public service

Digital Transformation is under constant evolution. Organizations that were not already created in the digital environment need to digitalize their services. The process used to do so may involve not only elements of technology, but also social, political and organizational aspects. While there is no holistic method to implement digital transformation, organizations learn from successful cases in order to build their own way to implement digital transformation. This paper presents the process through which a physically delivered service provided by the Brazilian federal government was transformed into a digital service. This was performed with a prototyping approach made of six steps: diagnose the service, analyze the service, identify the requirements, and elaborate, verify, and validate the prototype. To perform the digitalization, an automation tool was used, and there was constant interaction with the service provider. This article offers a detailed process to implement digitalization by means of prototyping, which can be used by other organizations to make services digital

Food insecurity in families with children under five years of age on the Brazil-Peru Amazon border

Food and nutrition security is the regular and permanent access to quality food in sufficient quantity. The aim of this study was to estimate the prevalence and factors associated with food insecurity in households with children under five in the Amazon frontier Brazil - Peru. The study was conducted in 352 households in Assis Brasil (Brazil) and 89 households Iñapari (Peru), finding a prevalence of food insecurity of 40.6 % and 38.2 % , respectively ( p = 0.856 ) . In Assis Brasil, having domicile with wood floors or land increased by 2.47 times the odds of food insecurity compared to cement fl oors, ceramic or quarry tiles . Belonging to the poorest tertile increased the chance of food insecurity in 6.04 times ( p < 0.001 ), and the increment of each new resident increased by 37 % the chance of food insecurity in the household . In Iñapari, only living in house made of wood or with a wood floor was associated with food insecurity, showing that income is still the main factor associated with food insecurity in the Amazonian borders

Inferences about the global scenario of human T-cell lymphotropic virus type 1 infection using data mining of viral sequences

Human T-cell lymphotropic virus type 1 (HTLV-1) is mainly associated with two diseases: tropical spastic paraparesis/HTLV-1-associated myelopathy (TSP/HAM) and adult T-cell leukaemia/lymphoma. This retrovirus infects five-10 million individuals throughout the world. Previously, we developed a database that annotates sequence data from GenBank and the present study aimed to describe the clinical, molecular and epidemiological scenarios of HTLV-1 infection through the stored sequences in this database. A total of 2,545 registered complete and partial sequences of HTLV-1 were collected and 1,967 (77.3%) of those sequences represented unique isolates. Among these isolates, 93% contained geographic origin information and only 39% were related to any clinical status. A total of 1,091 sequences contained information about the geographic origin and viral subtype and 93% of these sequences were identified as subtype “a”. Ethnicity data are very scarce. Regarding clinical status data, 29% of the sequences were generated from TSP/HAM and 67.8% from healthy carrier individuals. Although the data mining enabled some inferences about specific aspects of HTLV-1 infection to be made, due to the relative scarcity of data of available sequences, it was not possible to delineate a global scenario of HTLV-1 infection

Updated Insights into the Phylogenetics, Phylodynamics, and Genetic Diversity of Nipah Virus (NiV)

Nipah virus (NiV), a biosafety level 4 agent, was first identified in human clinical cases during an outbreak in 1998 in Malaysia and Singapore. While flying foxes are the primary host and viral vector, the infection is associated with a severe clinical presentation in humans, resulting in a high mortality rate. Therefore, NiV is considered a virus with an elevated epidemic potential which is further underscored by its recent emergence (September 2023) as an outbreak in India. Given the situation, it is paramount to understand the molecular dynamics of the virus to shed more light on its evolution and prevent potential future outbreaks. In this study, we conducted Bayesian phylogenetic analysis on all available NiV complete genomes, including partial N-gene NiV sequences (≥1000 bp) in public databases since the first human case, registered in 1998. We observed the distribution of genomes into three main clades corresponding to the genotypes Malaysia, Bangladesh and India, with the Malaysian clade being the oldest in evolutionary terms. The Bayesian skyline plot showed a recent increase in the viral population size since 2019. Protein analysis showed the presence of specific protein families (Hendra_C) in bats that might keep the infection in an asymptomatic state in bats, which also serve as viral vectors. Our results further indicate a shortage of complete NiV genomes, which would be instrumental in gaining a better understanding of NiV’s molecular evolution and preventing future outbreaks. Our investigation also underscores the critical need to strengthen genomic surveillance based on complete NiV genomes that will aid thorough genetic characterization of the circulating NiV strains and the phylogenetic relationships between the henipaviruses. This approach will better prepare us to tackle the challenges posed by the NiV virus and other emerging viruses

Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical training course in Brazil

Abstract The objective of this report was to describe the first face-to-face course aimed at training public health professionals in performing real-time genomic surveillance during the pandemic period. Experience report on a theoretical-practical course focusing on genomic research and surveillance, including mobile sequencing technologies, bioinformatics, phylogenetics and epidemiological modeling. There were 162 participants in the event and it was the first major face-to-face training course conducted during the COVID-19 epidemic in Brazil. No cases of SARS-CoV-2 infection was detected among the participants at the end of the event, suggesting the safety and effectiveness of all safety measures adopted. The results of this experience suggest that it is possible to conduct professional training safely during pandemics, as long as all safety protocols are followed