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 2 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 assignment tools to show that the proposed lineages are useful for regional, national, and subnational 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.

Viral metagenomics unveils MW (Malawi) polyomavirus infection in Brazilian pediatric patients with acute respiratory disease.

Viral metagenomics has been extensively applied for the identification of emerging or poorly characterized viruses. In this study, we applied metagenomics for the identification of viral infections among pediatric patients with acute respiratory disease, but who tested negative for SARS-CoV-2. Twelve pools composed of eight nasopharyngeal specimens were submitted to viral metagenomics. Surprisingly, in two of the pools, we identified reads belonging to the poorly characterized Malawi polyomavirus (MWPyV). Then, the samples composing the positive pools were individually tested using quantitative polymerase chain reaction for identification of the MWPyV index cases. MWPyV-positive samples were also submitted to respiratory virus panel testing due to the metagenomic identification of different clinically important viruses. Of note, MWPyV-positive samples tested also positive for respiratory syncytial virus types A and B. In this study, we retrieved two complete MWPyV genome sequences from the index samples that were submitted to phylogenetic inference to investigate their viral origin. Our study represents the first molecular and genomic characterization of MWPyV obtained from pediatric patients in South America. The detection of MWPyV in acutely infected infants suggests that this virus might participate (coparticipate) in cases of respiratory symptoms. Nevertheless, future studies based on testing of a larger number of clinical samples and MWPyV complete genomes appear to be necessary to elucidate if this emerging polyomavirus might be clinically important.

Epidemic history and evolution of an emerging threat of international concern, the severe acute respiratory syndrome coronavirus 2.

This comprehensive review focuses on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its impact as the cause of the COVID-19 pandemic. Its objective is to provide a cohesive overview of the epidemic history and evolutionary aspects of the virus, with a particular emphasis on its emergence, global spread, and implications for public health. The review delves into the timelines and key milestones of SARS-CoV-2's epidemiological progression, shedding light on the challenges encountered during early containment efforts and subsequent waves of transmission. Understanding the evolutionary dynamics of the virus is crucial in monitoring its potential for adaptation and future outbreaks. Genetic characterization of SARS-CoV-2 is discussed, with a focus on the emergence of new variants and their implications for transmissibility, severity, and immune evasion. The review highlights the important role of genomic surveillance in tracking viral mutations linked to establishing public health interventions. By analyzing the origins, global spread, and genetic evolution of SARS-CoV-2, valuable insights can be gained for the development of effective control measures, improvement of pandemic preparedness, and addressing future emerging infectious diseases of international concern.

Molecular identification of the emerging Human Gemykibivirus-2 (HuGkV-2) among Brazilian blood donors.

Human gemykibivirus-2 (HuGkV-2) belonging to the Gemykibivirus genus (Genomoviridae family) is an emerging DNA virus which has been described as a component of the virome of a wide variety of samples including clinical ones. So far, the HuGkV-2 DNA prevalence in the human population as well as its clinical impact are completely unknown. The objective of this study was to investigate the HuGkV-2 DNA prevalence among Brazilian healthy blood donors from three different geographic regions. A total of 450 blood samples were screened for HuGkV-2 DNA (150 samples were from the Brazilian Amazon, 150 from Midwest Brazil and 150 from South Brazil). The overall HuGkV-2 DNA prevalence was 7.8 %. Considering the examined regions, the highest prevalence was observed in the Brazilian Amazon (city of Macapa, state of Amapa), 15.3 %, followed by the Midwest Brazil (city of Brasilia, Federal District) (6.0 %) and South Brazil (city of Santa Maria, Rio Grande do Sul State) (2.0 %). This study gives preliminary insights on the molecular prevalence of HuGkV-2 DNA among Brazilian blood donors, highlighting that the highest HuGkV-2 prevalence was recorded in the Brazilian Amazon. However, more studies regarding the prevalence, transmission routes and any possible clinical effects appear to be crucial in order to understand the impact of this emerging viral agent.

A traveling SARS-CoV-2 laboratory as part of a pandemic response among vulnerable Brazilian populations.

BACKGROUND: Brazil has been dramatically hit by the SARS-CoV-2 pandemic and is a world leader in COVID-19 morbidity and mortality. Additionally, the largest country of Latin America has been a continuous source of SARS-CoV-2 variants and shows extraordinary variability of the pandemic strains probably related to the country´s outstanding position as a Latin American economical and transportation hub. Not all regions of the country show sufficient infrastructure for SARS-CoV-2 diagnosis and genotyping which can negatively impact the pandemic response. METHODS: Due to this reason and to disburden the diagnostic system of the inner São Paulo State, the Butantan Institute established the Mobile Laboratory (in Portuguese: LabMovel) for SARS-CoV-2 testing which started a trip of the most important "hotspots" of the most populous Brazilian region. The LabMovel initiated in two important cities of the State: Aparecida do Norte (an important religious center) and the Baixada Santista region which incorporates the port of Santos, the busiest in Latin America. The LabMovel was fully equipped with an automatized system for SARS-CoV-2 diagnosis and sequencing/genotyping. It also integrated the laboratory systems for patient records and results divulgation including in the Federal Brazilian Healthcare System. RESULTS: Currently,16,678 samples were tested, among them 1,217 from Aparecida and 4,564 from Baixada Santista. We tracked the delta introductio in the tested regions with its high diversification. The established mobile SARS-CoV-2 laboratory had a major impact on the Public Health System of the included cities including timely delivery of the results to the healthcare agents and the Federal Healthcare system, evaluation of the vaccination status of the positive individuals in the background of exponential vaccination process in Brazil and scientific and technological divulgation of the fieldwork to the most vulnerable populations. CONCLUSIONS: The SARS-CoV-2 pandemic has demonstrated worldwide the importance of science to fight against this viral agent and the LabMovel shows that it is possible to integrate researchers, clinicians, healthcare workers and patients to take rapid actions that can in fact mitigate this and other epidemiological situations.

SARS-COV-2 genomic monitoring in the state of São Paulo unveils two emerging AY.43 sublineages.

Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely-Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.

Monitoring of HTLV-1-associated diseases by proviral load quantification using multiplex real-time PCR.

Proviral load (PVL) is one of the determining factors for the pathogenesis and clinical progression of the human T-lymphotropic virus type I (HTLV-1) infection. In the present study, we optimized a sensitive multiplex real-time PCR for the simultaneous detection and quantification of HTLV-1 proviral load and beta-globin gene as endogenous control. The values obtained for HTLV-1 PVL were used to monitor the clinical evolution in HTLV-1-infected individuals. A vector containing cloned DNA targets of the real-time PCR for the beta-globin gene and the HTLV-1pol region was constructed. For the reaction validation, we compared the amplification efficiency of the constructed vector and MT-2 cell line containing HTLV-1. The analytical sensitivity of the reaction was evaluated by the application of a standard curve with a high order of magnitude. PVL assay was evaluated on DNA samples of HTLV-1 seropositive individuals. The construct showed adequate amplification for the beta-globin and HTLV-1 pol genes when evaluated as multiplex real-time PCR (slope = 3.23/3.26, Y-intercept = 40.18/40.73, correlation coefficient r2 = 0.99/0.99, and efficiency = 103.98/102.78, respectively). The quantification of PVL using the MT-2 cell line was equivalent to the data obtained using the plasmidial curve (2.5 copies per cell). In HTLV-1-associatedmyelopathy/tropical spastic paraparesis patients, PVL was significantly higher (21315 ± 2154 copies/105 PBMC) compared to asymptomatic individuals (1253 ± 691 copies/105 PBMC). The obtained results indicate that the optimized HTLV-1 PVL assay using plasmidial curve can be applied for monitoring and follow-up of the progression of HTLV-1 disease. The use of a unique reference plasmid for both HTLV-1 and endogenous gene allows a robust and effective quantification of HTLV-1 PVL. In addition, the developed multiplex real-time PCR assay was efficient to be used as a tool to monitor HTLV-1-infected individuals.

Chikungunya virus seroprevalence in asymptomatic blood donors during an outbreak in the Federal District of Brazil.

INTRODUCTION: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus belonging to the Togaviridae family. The symptomatic infection is characterised by acute febrile disease which generally results in severe arthralgia and myalgia, however, most of the CHIKV infections remain asymptomatic. CHIKV RNA detection in asymptomatic volunteers may be responsible for the transfusion transmission of this infection, especially during outbreaks. There is no information for CHIKV seroprevalence among blood donors from the Federal District of Brazil. AIM: In early 2019, the Federal District of Brazil experienced a CHIKV outbreak, and this study evaluates the anti-CHIKV IgM and IgG presence in a well characterised cohort of blood donors from this region. METHODOLOGY: Blood samples were collected from 450 volunteer blood donors during a CHIKV outbreak and tested for the presence of anti-CHIKV IgG and IgM antibodies using ELISA. RESULTS: The CHIKV seroprevalence was 0.89% (n = 4/450) and anti-CHIKV IgM prevalence was 1.11% (n = 5/450). CONCLUSION: The obtained results demonstrated that at least some of the blood donors have experienced CHIKV infection which can be related to a hypothetical risk of CHIKV transfusion transmission. More studies are necessary in order to examine the impact of CHIKV on blood transfusion.

Virome comparison of deferred blood donations obtained from different geographic regions in the Sao Paulo State, Brazil.

The virome composition of blood units deferred due to symptomatic disease of the donors reported after blood donation may reveal novel or unsuspected viral agents which may have impact in the area of hemotherapy. The objective of this study was to compare the virome of blood donations obtained from two distantly located blood collecting institutions in the Saqo Paulo State and deferred from use due to post donation illness reports (PDIR). Plasma samples with PDIR due to different symptoms were collected in two cities of the Sao Paulo State (Sao Paulo city, 28 samples and Ribeirao Preto city, 11 samples). The samples were assembled in pools and sequenced in Illumina NextSeq 550 sequencer. The obtained raw sequencing data was analyzed using bioinformatic pipeline aiming viral identification. Phylogenetic classification of the most important contigs was also performed. The virome composition of the plasma samples obtained in both cities was different. This was more pronounced for some specific anellovirus types and the human pegivirus-1 (HPgV-1) which were exclusively found among donations obtained from the city of Sao Paulo. On the other hand, in PDIR samples from Ribeirao Preto, Dengue -2 reads were more abundant compared to commensal viral representatives. The obtained virome findings show that the differential viral abundance is related to geographic localization and specific disease endemicity. The virome of PDIR samples may be used to more profoundly analyze the hypothetic transfusion threats in a given location.

Detection of Influenza A(H3N2) Virus RNA in Donated Blood.

Influenza A virus infection has rarely been documented to cause viremia. In 28 blood donations in Brazil that were deferred because of postdonation information, we identified influenza A(H3N2) virus RNA in 1 donation using metagenomic analysis. Our finding implies theoretical risk for viremia and transfusion transmission.

Molecular prevalence and genotypes of human pegivirus-1 (HPgV-1) and SENV-like viruses among multiply transfused patients with beta-thalassemia.

Due to the high number of transfusions which patients with hereditary hemoglobinopathies (thalassemia, sickle cell disease) receive, they represent high risk of acquiring parenterally transmitted infectious diseases. In this respect, non pathogenic human commensal viruses, which also demonstrate parenteral transmission routes might also be acquired. One of the most widely spread parenterally-transmitted human commensal viruses include the Human Pegivirus-1 (HPgV-1, GBV-C) and Torque teno viruses (TTV) including its SEN virus-like (SENV) forms. The objective of this study was to evaluate the prevalence of HPgV-1 RNA and SENV-like viruses, among a group of patients with beta-thalassemia from a Blood Transfusion Center in the São Paulo State, Brazil. The prevalence of HPgV-1 RNA was 14.3 % (n = 6/42) and all of the positive samples were characterized as belonging to genotype 2 (83.3 % were referred to subgenotype 2A and 16.7 % to 2B). The prevalence of SENV-like viruses was 28.6 % (n = 12/42). SENV-like viruses of the genotypes SENV-H and SENV-A were classified during the performed phylogenetic analysis. Our study came as a continuation of a viral metagenomic survey among multiple transfused patients with beta-thalassemia. The obtained results shed a light on the prevalence and genotype distribution of commensal parenterally transmitted viruses like HPgV-1 and SENV in this specific population. However, more studies are needed to evaluate the clinical impact of these apparently non-pathogenic viruses in patients with thalassemia and their significance for the hemotherapy.

Human pegivirus-1 (HPgV-1, GBV-C) RNA prevalence and genotype diversity among volunteer blood donors from an intra-hospital hemotherapy service in Southern Brazil.

OBJECTIVE: Human pegivirus (HPgV-1, GBV-C) is classified within the Pegivirus genus of the Flaviviriade family. The natural history of HPgV-1 infection is still unclear, however, the main route of viral transmission seems to be the parenteral one. The detection of HPgV-1 viremia in blood donors without parenteral exposure demonstrates that other routes of HPgV-1 transmission might also exist. The objective of the present study was to evaluate the prevalence of HPgV-1 RNA and circulating genotypes among blood donors from a intra-hospital Hemotherapy Service localized in the Santa Maria city, central part of the Rio Grande do Sul State in the extreme South of Brazil. METHODS: Blood samples were obtained from 373 volunteer blood donors and tested for the presence of HPgV-1 RNA. All positive for RNA samples were submitted to sequencing and phylogenetic analysis. RESULTS: The prevalence of the HPgV-1 RNA was 5.9% (22/373). The performed phylogenetic analysis demonstrated a predominant detection of genotype 2 with its both subgenotype forms (95.5% of all isolates i.e 54.5% belonging to subgenotype 2 A and 40.9% belonging to subgenotype 2B). Only one sequence was classified as genotype 3 (1/22, 4.5%). CONCLUSIONS: Our study demonstrates the circulation pattern and genotypes of HPgV-1 among volunteer blood donors of South Brazil, and adds to the global knowledge of the natural history and possible transmission routes of this viral agent with putative impact on the area of hemotherapy.

Simultaneous zika and dengue serotype-4 viral detection and isolation from a donor plasma unit.

During zika and dengue viruse (ZIKV and DENV) outbreaks, the majority of the infected individuals remain clinically asymptomatic. Such asymptomatic individuals may occasionally acquire both arboviruses, donate blood, and contaminate haemoderivatives. The aim of this study was to characterize a ZIKV/DENV-4 coinfection in asymptomatic blood donor who donated blood during a large mixed ZIKV/DENV outbreak in the Säo Paulo State, Brazil. On the basis of post-donation information, one blood donor sample was found positive for ZIKV and DENV RNA. The DENV molecular serotyping was performed by molecular testing. The sample was also titrated on VERO E6 cells in order to define the presence of infectious arboviruses. The real-time PCR testing of the blood donor sample demonstrated very high viral load for both ZIKV and DENV. Further, molecular serotyping of DENV showed that the presence of DENV-4. The viral titration in cell culture indicated a titre of 2.75x10[6] PFU/ml which was concordant with the presence of infectious viruses in the blood donation. This is an interesting report for the simultaneous presence of infectious ZIKV and DENV-4 in asymptomatic blood sample. Special attention must be paid during mixed arboviral outbreaks for the possibility of transfusion-transmission of multiple arboviral agents.

Human parvovirus 4 prevalence among HTLV-1/2 infected individuals in Brazil.

Human parvovirus 4 (PARV4), a Tetraparvovirus, has been largely found in HIV, HBV, or HCV infected individuals. However, there is no data for the PARV4 occurrence in Human T-lymphotropic virus (HTLV-1/2) infected individuals, despite similar transmission routes. Here, PARV4 viremia was evaluated in 130 HTLV infected patients under care of a Brazilian HTLV outpatient clinic. PARV4 viremia was detected in 6.2% of the HTLV-1 infected patients. Most PARV4 positives showed no evidence for parenterally transmitted infections. It is suggested that in Brazil, transmission routes of PARV4 are more complex than in Europe and North America and resemble those in Africa. J. Med. Virol. 89:748-752, 2017. © 2016 Wiley Periodicals, Inc.

Development and optimization of a sensitive TaqMan® real-time PCR with synthetic homologous extrinsic control for quantitation of Human cytomegalovirus viral load.

Human cytomegalovirus (Human herpesvirus 5, HCMV) causes frequent asymptomatic infections in the general population. However, in immunosuppressed patients or congenitally infected infants, HCMV is related to high morbidity and mortality. In such cases, a rapid viral detection is crucial for monitoring the clinical outcome and the antiviral treatment. In this study, we optimized a sensitive biplex TaqMan® real-time PCR for the simultaneous detection and differentiation of a partial HCMV UL97 sequence and homologous extrinsic control (HEC) in the same tube. HEC was represented by a plasmid containing a modified HCMV sequence retaining the original primer binding sites, while the probe sequence was substituted by a phylogenetically divergent one (chloroplast CF0 subunit plant gene). It was estimated that the optimal HEC concentration, which did not influence the HCMV amplification is 1,000 copies/reaction. The optimized TaqMan® PCR demonstrated high analytical sensitivity (6.97 copies/reaction, CI = 95%) and specificity (100%). Moreover, the reaction showed adequate precision (repeatability, CV = 0.03; reproducibility, CV = 0.0027) and robustness (no carry-over or cross-contamination). The diagnostic sensitivity (100%) and specificity (97.8%) were adequate for the clinical application of the molecular platform. The optimized TaqMan® real-time PCR is suitable for HCMV detection and quantitation in predisposed patients and monitoring of the applied antiviral therapy. J. Med. Virol. 88:1604-1612, 2016. © 2016 Wiley Periodicals, Inc.

No evidence of xenotropic murine leukemia virus-related virus infection in Brazilian multiply transfused patients with sickle cell disease and beta-thalassemia major.

Although xenotropic murine leukemia virus-related virus (XMRV) has been regarded as a laboratory contaminant, it remains one of the most controversial viruses. The objective of the study was to determine if XMRV is present in 44 patients with beta-thalassemia major, 48 with sickle cell disease, and 89 volunteer blood donors. After RNA/ DNA extraction from plasma/buffy coat the samples were screened for XMRV sequences by conserved nested GAG primers. None of the RNA samples showed a positive result. Surprisingly, four DNA samples obtained from blood donors were positive for XMRV provirus. The subsequent phylogenetic analysis revealed that these sequences are identical to the positive control (murine leukemia retrovirus) and are probably consistent with laboratory contamination. XMRV infection (provirus and viral RNA) was absent in multiply transfused patients and volunteer blood donors. The positive result obtained from some blood donors probably reflects laboratory contamination. We believe that XMRV does not pose risk to blood transfusion.

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.

Effect of Interindividual Variability in Metabolic Clearance and Relative Bioavailability on Rifampicin Exposure in Tuberculosis Patients with and without HIV Co-Infection: Does Formulation Quality Matter?

The present study aims to characterise the pharmacokinetics of rifampicin (RIF) in tuberculosis (TB) patients with and without HIV co-infection, considering the formation of 25-O-desacetyl-rifampicin (desRIF). It is hypothesised that the metabolite formation, HIV co-infection and drug formulation may further explain the interindividual variation in the exposure to RIF. Pharmacokinetic, clinical, and demographic data from TB patients with (TB-HIV+ group; n = 18) or without HIV (TB-HIV- group; n = 15) who were receiving RIF as part of a four-drug fixed-dose combination (FDC) regimen (RIF, isoniazid, pyrazinamide, and ethambutol) were analysed, along with the published literature data on the relative bioavailability of different formulations. A population pharmacokinetic model, including the formation of desRIF, was developed and compared to a model based solely on the parent drug. HIV co-infection does not alter the plasma exposure to RIF and the desRIF formation does not contribute to the observed variability in the RIF disposition. The relative bioavailability and RIF plasma exposure were significantly lower than previously reported for the standard regimen with FDC tablets. Furthermore, participants weighting less than 50 kg do not reach the same RIF plasma exposure as compared to those weighting >50 kg. In conclusion, as no covariate was identified other than body weight on CL/F and Vd/F, low systemic exposure to RIF is likely to be caused by the low bioavailability of the formulation.