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Epstein–Barr virus (EBV) is a ubiquitous gammaherpesvirus etiologically associated with benign and malignant diseases. Since the pathogenic mechanisms of EBV are not fully understood, understanding EBV genetic diversity is an ongoing goal. Therefore, the present work describes the genetic diversity of the lytic gene BZLF1 in a sampling of 70 EBV-positive cases from southeastern Brazil. Additionally, together with the genetic regions previously characterized, the aim of the present study was to determine the impact of viral genetic factors that may influence EBV genetic diversity. Accordingly, the phylogenetic analysis of the BZLF1 indicated two main clades with high support, BZ-A and BZ-B (PP > 0.85). Thus, the BZ-A clade was the most diverse clade associated with the main polymorphisms investigated, including the haplotype Type 1 + V3 (p < 0.001). Furthermore, the multigene phylogenetic analysis (MLA) between BZLF1 and the oncogene LMP1 showed specific clusters, revealing haplotypic segregation that previous single-gene phylogenies from both genes failed to demonstrate. Surprisingly, the LMP1 Raji-related variant clusters were shown to be more diverse, associated with BZ-A/B and the Type 2/1 + V3 haplotypes. Finally, due to the high haplotypic diversity of the Raji-related variants, the number of DNA recombination-inducing motifs (DRIMs) was evaluated within the different clusters defined by the MLA. Similarly, the haplotype BZ-A + Raji was shown to harbor a greater number of DRIMs (p < 0.001). These results call attention to the high haplotype diversity of EBV in southeast Brazil and strengthen the hypothesis of the recombinant potential of South American Raji-related variants via the LMP1 oncogene. [ABSTRACT FROM AUTHOR]

This study investigated the prevalence and genetic diversity of gastroenteric viruses in mussels and oysters in Rio de Janeiro, Brazil. One hundred and thirty-four marketed bivalve samples were obtained between January and December 2022. The viral analysis was performed according to ISO/TS 15216, and the screening revealed the detection of norovirus GII/GI (40.3%), sapovirus (SaV; 12.7%), human mastadenovirus (7.5%), and rotavirus A (RVA; 5.9%). In total, 44.8% (60) of shellfish samples tested positive for one or more viruses, 46.7% (28/60) of the positive samples tested positive for a single viral agent, 26.7% (16) tested positive for two viral agents, 8.3% (5) for three viral agents, and 13.3% (8) for four viral agents. Additionally, three mussel samples were contaminated with the five investigated viruses (5%, 3/60). Norovirus GII showed the highest mean viral load (3.4 × 105 GC/g), followed by SaV (1.4 × 104 GC/g), RVA (1.1 × 104 GC/g), human mastadenovirus (3.9 × 103 GC/g), and norovirus GI (6.7 × 102 GC/g). Molecular characterization revealed that the recovered norovirus strains belonged to genotypes GII.2, GII.6, GII.9, GII.17, and GII.27; SaV belonged to genotypes GI.1 and GIV.1; RVA to genotypes G6, G8, P[8]-III, and human mastadenovirus to types F40 and F41. The GII.27 norovirus characterized in this study is the only strain of this genotype reported in Brazil. This study highlights the dissemination and diversity of gastroenteric viruses present in commercialized bivalves in a touristic area, indicating the potential risk to human health and the contribution of bivalves in the propagation of emerging pathogens. [ABSTRACT FROM AUTHOR]

Since emerging in French Polynesia and Brazil in the 2010s, Zika virus (ZIKV) has been associated with fetal congenital disease. Previous studies have compared ancestral and epidemic ZIKV strains to identify strain differences that may contribute to vertical transmission and fetal disease. However, within-host diversity in ZIKV populations during vertical transmission has not been well studied. Here, we used the established anti-interferon treated Rag1-/- mouse model of ZIKV vertical transmission to compare genomic variation within ZIKV populations in matched placentas, fetal bodies, and fetal brains via RNASeq. At early stages of vertical transmission, the ZIKV populations in the matched placentas and fetal bodies were similar. Most ZIKV single nucleotide variants were present in both tissues, indicating little to no restriction in transmission of ZIKV variants from placenta to fetus. In contrast, at later stages of fetal infection there was a sharp reduction in ZIKV diversity in fetal bodies and fetal brains. All fetal brain ZIKV populations were comprised of one of two haplotypes, containing either a single variant or three variants together, as largely homogenous populations. In most cases, the dominant haplotype present in the fetal brain was also the dominant haplotype present in the matched fetal body. However, in two of ten fetal brains the dominant ZIKV haplotype was undetectable or present at low frequencies in the matched placenta and fetal body ZIKV populations, suggesting evidence of a strict selective bottleneck and possible selection for certain variants during neuroinvasion of ZIKV into fetal brains. Author summary: Zika virus (ZIKV) is known to cause congenital disease in humans through vertical transmission of the virus from mothers to fetuses during pregnancy. How the virus populations change during this process is currently not well understood. To evaluate differences in ZIKV populations during vertical transmission, we infected pregnant mice with ZIKV and sequenced the viral populations from matched placentas and fetal bodies at early stages of vertical transmission, and matched placentas, fetal bodies, and fetal brains at late stages of vertical transmission when the virus enters the fetal brain. We determined that there is little restriction of ZIKV diversity during transmission from the placenta to the fetus at early stages. However, there was a sharp decrease in ZIKV diversity in both fetal bodies and fetal brains at late stages. Two predominant viral variants were found across all fetal brains and most fetal bodies at late stages, suggesting there may be possible selection for certain variants during neuroinvasion of ZIKV into fetal brains. [ABSTRACT FROM AUTHOR]

Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease in the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many genetic types, and lineages are described worldwide. IBV genetic type I—strain 23 (GI‐23) has spread across different continents (including Asia, Europe and Africa), causing multiple outbreaks and severe economic losses throughout the poultry industry in the last decade. The present study aimed to report the emergence and molecular characterization of GI‐23 in South Brazil, being detected for the first time in South America. Eighty‐two broiler flocks presenting clinical suspicion of infectious bronchitis were selected for this study. Tracheal, renal and intestinal samples were collected for IBV detection and genotyping. A total of 57 flocks were positive for IBV by generic RT‐qPCR targeting 5' untranslated region and 31 also tested positive for GI‐11 by a specific RT‐qPCR targeting S1 gene for this lineage. The remaining 26 IBV‐positive samples were genotyped by partial and one by complete S1 gene/protein sequencing. Phylogenetic analysis demonstrated that all of them clustered into a specific branch of the GI‐23. S1 protein sequence analysis evidenced that all Brazilian GI‐23 IBVs had the two characteristic amino acid substitutions A93T and S/H118P/L, but other changes were also observed, such as S37F (n = 21; 81%), G117S (n = 17, 65%), P122S (n = 16; 61%) and W71R (n = 9; 35%). This study brings new insights into the epidemiology of the IBV GI‐23 in the world, highlighting its emergence and molecular characteristics in Brazil, South America. [ABSTRACT FROM AUTHOR]

The recent reemergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the rapid dissemination of the virus in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil, we generated 18 complete and nearly complete genomes from the peak of the epidemic curve from nonhuman primates (NHPs) and human infected cases across the Espírito Santo and Rio de Janeiro states. Genomic sequencing of 18 YFV genomes revealed the estimated timing, source, and likely routes of yellow fever virus transmission and dispersion during one of the largest outbreaks ever registered in Brazil. We showed that during the recent epidemic, YFV was reintroduced from Minas Gerais to the Espírito Santo and Rio de Janeiro states multiple times between 2016 and 2019. The analysis of data from portable sequencing could identify the corridor of spread of YFV. These findings reinforce the idea that continued genomic surveillance strategies can provide information on virus genetic diversity and transmission dynamics that might assist in understanding arbovirus epidemics. [ABSTRACT FROM AUTHOR]

In Brazil, most studies of intra-type variants of human papillomavirus (HPV) have focused on HPV16 and HPV18, but other high-risk HPV types have not been studied. Here, we report the prevalence of lineages and variants of HPV35, HPV45 and HPV58 in cervical cancers from the Amazonian and Southeast Brazilian regions. The most frequent sublineages were A1 for HPV35, B2 for HPV45, and A2 for HPV58. The Southeast region had a higher frequency of the B2 sublineage of HPV45, and for HPV35, the genetic and nucleotide sequence diversity were higher in the Southeast region, suggesting that regional factors are influencing the diversity and lineage prevalence. [ABSTRACT FROM AUTHOR]

Insects originated more than 400 million years ago and have undergone since then an extraordinary diversification, associated with many spectacular innovations, such as flying or establishment of social societies. They have colonized all terrestrial ecosystems, and are exposed to a broad range of pathogens, including viruses, bacteria, fungi, and parasites. Like all animals, insects rely on innate immunity to control infections. Innate immunity is the first layer in host-defense in animals. It involves receptors sensing the presence of infectious microorganisms and triggering signaling that leads to the expression of genes coding effector molecules, which concur to counter the infection. In vertebrates, a subset of genes induced encode cytokines and coreceptors that activate a second layer of host defense known as adaptive immunity. The study of the innate immunity in insects has led to:. – the discovery of antimicrobial peptides, which target bacteria and fungi and are now known to be present in all animals and in plants; – the identification of evolutionarily conserved important genes activating innate immunity, e.g., the Toll-like receptors; – a better understanding of viral and parasitic diseases transmitted by hematophagous vector insects. Among infectious microbes, viruses represent a particular threat because they offer few intrinsic targets for inhibition by antiviral molecules. This is because they consist in their simplest form in a nucleic acid encapsulated in a protein shell, and hijack molecular machineries from host cells to complete their replication cycle. Of note, recent advances in high-throughput sequencing (HTS) technologies have opened the way to the characterization of the virome (i.e. the genetic diversity of viruses in a biological sample) in insects. Interestingly, these studies revealed that: – infection by one or more viruses is common in arthropods; – the genetic diversity of arthropod viruses surpasses that described previously; – the genetic diversity of viruses found in plants and vertebrate animals fall within the genetic diversity of viruses associated with arthropods [1]. This suggests that arthropods may have participated in the evolution of viruses causing human disease and points to the relevance of characterizing antiviral mechanisms in insects. One reason to investigate insect–virus interactions is that hematophagous insects, for example Aedes mosquitoes, are vectors of important viral diseases such as Zika, dengue, yellow fever, and chikungunya. RNA interference is an RNA-based mechanism that offers broad protection against viruses in insects. This elegant mechanism relies on the recognition of double + stranded (ds) viral RNAs by the RNase III enzyme Dicer-2, which processes them into 21 nucleotide long small interfering (si) RNA duplexes. One strand of the siRNA is then loaded onto the RNAse H-like enzyme Argonaute 2, where it serves as a guide to specifically target viral RNAs. Of note, virus-derived siRNAs, which provide a footprint of the action of the insect immune system, can be characterized by HTS. In collaboration with the group of Prof. Joao Marques (UFMG, Belo Horizonte, Brazil), we have shown that small RNA sequencing allows assembling longer contigs of viral RNAs, generating a better coverage of viral genomes, than traditional long RNA sequencing. In addition, the profile of the small RNAs is characteristic of the virus from which they derive (e.g., number of reads, size distribution of the small RNAs). For example, some viruses infect the ovaries and generate a different type of small RNAs, known as Piwi-interacting RNAs, or piRNAs, which are longer (24–28nt) than siRNAs (Fig. 1). As a result, it is possible to assign a viral origin to sequences even if they do not exhibit any homology to sequences present in the databases. This represents a significant improvement in the characterization of the insect virome [2]. We have applied this strategy to wild Aedes mosquitoes collected in a dengue endemic region in Brazil, and have identified three viruses. Two of them, the Bunyavirus Phasi Charoen-like virus (PCLV) and the unclassified virus Humaita-Tubiacanga virus (HTV), have a high prevalence in Aedes mosquitoes collected in different regions of Brazil. These poorly characterized viruses may affect the dynamics of transmission of known viral pathogens such as dengue, Zika, or chikungunya viruses, a hypothesis that is currently being tested in the laboratory. The discovery of the important role played by Toll-like receptors in innate immunity revealed that important gene regulatory networks have been conserved during evolution and illustrated how studies in insects can lead to important findings for the biomedical field. This has provided strong incentives to identify and characterize other evolutionarily conserved host-defense mechanisms. As a consequence, the contribution of non-conserved genes to insect immunity has received less attention. Yet, these genes may be just as important as the conserved genes. Indeed, insects evolved independently of mammals for several hundreds of thousands of years, which provided multiple opportunities to develop original strategies of defense against infections. Hence, the characterization of insect-specific antiviral factors may inspire new strategies to counter infections. For example, we recently characterized the gene diedel , which is strongly induced following viral infection in Drosophila , and has been hijacked at least three times by insect DNA viruses. We showed that diedel encodes a circulating protein that suppresses the activity of the immune deficiency (IMD) pathway of host-defense. The IMD pathway is one of the two major innate immunity pathways regulating transcription factors of the NF-κB family in flies. The discovery that several insect viruses have hijacked a cellular gene suppressing the IMD pathway prompted us to investigate its contribution to the control of viral infections. Interestingly, we discovered that two components of the pathway, the kinase IKKβ and the NF-κB transcription factor Relish, are required to restrict infection by two picorna-like viruses, Drosophila C Virus (DCV) and Cricket Paralysis Virus (CrPV) in Drosophila. By contrast, the other components of the pathway, including the regulatory subunit of the IKKβ kinase, NEMO, do not appear to play a role in the resistance to infection by these viruses. Among the genes regulated by IKKβ in virus-infected flies, we identified two genes involved in the resistance to viral infection. The first one is the homologue of the mammalian factor STING (Stimulator of Interferon Genes), and we could show that it acts upstream of IKKβ and Relish in a new signaling pathway (Fig. 2). The second one encodes a new antiviral factor, that we called Nazo (meaning "enigma" in Japanese) [3]. The STING-IKKβ-Relish signaling cassette controls inducible expression of Nazo in response to viral infection. Nazo results from a duplication of the gene CG3740 in Drosophila species from the Sophophora subgenus. Of note, CG3740 is not upregulated by viral infection, and ectopic expression of the gene has no effect on replication of DCV or CrPV, unlike expression of Nazo , which results in strong suppression of viral replication. The discovery of Nazo provides an excellent opportunity to decipher the genetics by which a cellular gene acquires a new function in antiviral immunity. Furthermore, the characterization of its mode of action against picorna-like viruses may reveal novel angles of attack against a family of viruses that include many serious human pathogens (e.g., poliovirus). In summary, the fantastic diversity of insects extends to the viruses they carry, and to the genetic mechanisms they evolved to control these viruses. This biodiversity provides a unique opportunity to extend the repertoire of known antiviral mechanisms and to identify weak spots in the replication cycles of viruses. [ABSTRACT FROM AUTHOR]

A high diversity of begomoviruses that infect non-cultivated plants has been noted in Brazil. Here, we report the complete sequences of two new species of bipartite begomoviruses from Sida sp. plants collected in the state of Piauí, northeastern Brazil. The genomes of these viruses show a genomic organization that is typical of New World begomoviruses. In phylogenetic analysis, two closely related viruses (sida angular mosaic virus, SiAMV and sida chlorotic vein virus, SiCVV) clustered with other begomoviruses described in tomato and Sida plants in Brazil. Evidence of recombination is shown among isolates of the species described. [ABSTRACT FROM AUTHOR]

Almost two decades after the isolation of the first amoebal giant viruses, indubitably the discovery of these entities has deeply affected the current scientific knowledge on the virosphere. Much has been uncovered since then: viruses can now acknowledge complex genomes and huge particle sizes, integrating remarkable evolutionary relationships that date as early as the emergence of life on the planet. This year, a decade has passed since the first studies on giant viruses in the Brazilian territory, and since then biomes of rare beauty and biodiversity (Amazon, Atlantic forest, Pantanal wetlands, Cerrado savannas) have been explored in the search for giant viruses. From those unique biomes, novel viral entities were found, revealing never before seen genomes and virion structures. To celebrate this, here we bring together the context, inspirations, and the major contributions of independent Brazilian research groups to summarize the accumulated knowledge about the diversity and the exceptionality of some of the giant viruses found in Brazil. [ABSTRACT FROM AUTHOR]

Dengue virus (DENV) is a mosquito-borne viral pathogen that plagues many tropical-climate nations around the world, including Brazil. Molecular epidemiology is a growing and increasingly invaluable tool for understanding the dispersal, persistence, and diversity of this impactful virus. In this study, plasma samples (n = 824) from individuals with symptoms consistent with an arboviral febrile illness were analyzed to identity the molecular epidemiological dynamics of DENV circulating in the Brazilian state of Amapá. Twelve DENV type 1 (DENV-1) genomes were identified, which were phylogenetically related to the BR4 lineage of genotype V. Phylodynamics analysis suggested that DENV-1 BR-4 was introduced into Amapá around early 2010, possibly from other states in northern Brazil. We also found unique amino acids substitutions in the DENV-1 envelope and NS5 protein sequences in the Amapá isolates. Characterization of the DENV-1 BR-4 sequences highlights the potential of this new lineage to drive outbreaks of dengue in the Amazon region. [ABSTRACT FROM AUTHOR]

The Chikungunya virus infection in Brazil has raised several concerns due to the rapid dissemination of the virus and its association with several clinical complications. Nevertheless, there is limited information about the genomic epidemiology of CHIKV circulating in Brazil from surveillance studies. Thus, to better understand its dispersion dynamics in Rio de Janeiro (RJ), one of the most affected states during the 2016–2019 epidemic waves, we generated 23 near-complete genomes of CHIKV isolates from two main cities located in the metropolitan mesoregion, obtained directly from clinical samples. Our phylogenetic reconstructions suggest the 2019-CHIKV-ECSA epidemic in RJ state was characterized by the co-circulation of multiple clade (clade A and B), highlighting that two independent introduction events of CHIKV-ECSA into RJ state have occurred between 2016–2019, both mediated from the northeastern region. Interestingly, we identified that the two-clade displaying eighteen characteristic amino acids changes among structural and non-structural proteins. Our findings reinforce that genomic data can provide information about virus genetic diversity and transmission dynamics, which might assist in the arbovirus epidemics establishing of an effective surveillance framework. [ABSTRACT FROM AUTHOR]

Giant viruses are complex members of the virosphere, exhibiting outstanding structural and genomic features. Among these viruses, the pandoraviruses are some of the most intriguing members, exhibiting giant particles and genomes presenting at up to 2.5 Mb, with many genes having no known function. In this work, we analyzed, by virological and microscopic methods, the replication cycle steps of three new pandoravirus isolates from samples collected in different regions of Brazil. Our data indicate that all analyzed pandoravirus isolates can deeply modify the Acanthamoeba cytoplasmic environment, recruiting mitochondria and membranes into and around the electron-lucent viral factories. We also observed that the viral factories start forming before the complete degradation of the cellular nucleus. Various patterns of pandoravirus particle morphogenesis were observed, and the assembly of the particles seemed to be started either by the apex or by the opposite side. On the basis of the counting of viral particles during the infection time course, we observed that pandoravirus particles could undergo exocytosis after their morphogenesis in a process that involved intense recruitment of membranes that wrapped the just-formed particles. The treatment of infected cells with brefeldin affected particle exocytosis in two of the three analyzed strains, indicating biological variability among isolates. Despite such particle exocytosis, the lysis of host cells also contributed to viral release. This work reinforces knowledge of and reveals important steps in the replication cycle of pandoraviruses. IMPORTANCE The emerging Pandoraviridae family is composed of some of the most complex viruses known to date. Only a few pandoravirus isolates have been described until now, and many aspects of their life cycle remain to be elucidated. A comprehensive description of the replication cycle is pivotal to a better understanding of the biology of the virus. For this report, we describe new pandoraviruses and used different methods to better characterize the steps of the replication cycle of this new group of viruses. Our results provide new information about the diversity and biology of these giant viruses., (Copyright © 2019 American Society for Microbiology.)