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

Pegivirus Detection in Cerebrospinal Fluid from Patients with Central Nervous System Infections of Unknown Etiology in Brazil by Viral Metagenomics

Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for understanding their spread, managing outbreaks, and effective patient care. In a study conducted in the state of São Paulo, Brazil, cerebrospinal fluid (CSF) samples from 500 patients with CNS diseases of indeterminate etiology, collected between 2017 and 2021, were analyzed. Employing a mNGS approach, we obtained the complete coding sequence of Pegivirus hominis (HPgV) genotype 2 in a sample from a patient with encephalitis (named IAL-425/BRA/SP/2019); no other pathogen was detected. Subsequently, to determine the extent of this virus's presence, both polymerase chain reaction (PCR) and/or real-time PCR assays were utilized on the entire collection. The presence of the virus was identified in 4.0% of the samples analyzed. This research constitutes the first report of HPgV detection in CSF samples in South America. Analysis of the IAL-425 genome (9107 nt) revealed a 90% nucleotide identity with HPgV strains from various countries. Evolutionary analyses suggest that HPgV is both endemic and extensively distributed. The direct involvement of HPgV in CNS infections in these patients remains uncertain.

Hepatitis C and Human Pegivirus Coinfection in Patients with Chronic Hepatitis C from the Brazilian Amazon Region: Prevalence, Genotypes and Clinical Data

Coinfection of HPgV-1 with hepatitis C virus (HCV) is common due to shared modes of transmission, with a prevalence of HPgV-1 viremia of approximately 20% among individuals with chronic HCV infection. The aim of the present study was to estimate the prevalence of HPgV-1 RNA and circulating genotypes in patients with hepatitis C from a health service located in the city of Belém, in the state of Pará, Northern Brazil. A total of 147 samples were included in the study from February to December 2019. Among the participants, 72.1% (106/147) were monoinfected with HCV, with detectable HCV viral RNA, and 27.9% (41/147) were coinfected with HCV/HPgV-1. The most frequently found genotypes were HPgV-1 genotypes 1 and 2 (36.6% and 63.4%), respectively. While for HCV there was a predominance of genotypes 1 and 3 (58.5% and 41.5%). No significant differences were found when comparing any risk, sociodemographic, or clinical factors between groups. Also, there was no statistically significant difference when relating the viral genotypes of both agents. This study indicated that the prevalence of infection by HPgV-1 is high in HCV carriers in Belém, Pará, and probably does not change the clinical course of HCV infection, however, further studies are still needed.

Human Pegivirus-1 Detection and Genotyping in Brazilian Patients with Fulminant Hepatitis

Fulminant hepatitis is a severe clinical disease characterized by a marked decline in liver function and encephalopathy. In a previous survey, using metagenomics in a group of 27 patients with this clinical condition, we observed an expressive quantity of reads of the Human pegivirus-1 (HPgV-1). Therefore, the objective of this study was to evaluate the frequency, molecular features, and HPgV-1 circulating genotypes in patients with fulminant hepatitis. After testing the collected plasma samples, we discovered twelve samples (44.4%) that were positive for HPgV-1 RNA (using both real-time and nested PCR). The positive samples presented a mean cycle threshold (Ct) of 28.5 (±7.3). Genotyping assignments revealed that all HPgV-1 positive samples belonged to the HPgV-1 genotype 2 (both subgenotypes 2A and 2B were identified). Although HPgV-1 is considered a commensal virus, little is known regarding its prevalence and genotypes in cases of fulminant hepatitis. More research is needed to understand whether HPgV-1 can be implicated in clinical disorders and infectious diseases.

Regional mutations in CHIKV-ECSA genomes and detection of other viruses in the serum of acute febrile patients by a metagenomic approach in Mato Grosso, Central-Western Brazil, 2018

Mato Grosso (MT) State is part of central western Brazil and has a tropical permissive environment that favors arbovirus outbreaks. A metagenomic approach was used to identify viral genomes in seven pools of serum from patients (n=65) with acute febrile disease. Seven chikungunya virus (CHIKV) genomes were determined, showing four amino acid changes found only in CHIKV genomes obtained in MT since 2018: nsP2:T31I, nsP3: A388V, E3:T201I and E3:H57R, in addition to other mutations in E1, nsP2 and nsP4. Six parvovirus B19 (B19V) genotype I genomes (4771-5131 nt) showed four aa alterations (NS1:N473D, R579Q; VP1:I716T; and 11 kDa:V44A) compared to most similar B19V from the USA. Coinfection between CHIKV and B19V was evidenced in 22/65 (33.8%) patients by RT‒PCR and PCR, respectively. Other viruses found in these pools include human pegivirus C, torque teno virus 3, an unclassified TTV and torque teno mini virus. Metagenomics represents a useful approach to detect viruses in the serum of acute febrile patients suspected of arbovirus disease.

Screening of febrile patients with suspected malaria from the Brazilian Amazon for virus infection

Arthropod-borne viruses (arboviruses) are a significant public health threat, especially in tropical and subtropical regions. More than 150 arboviruses can cause febrile illness following infection in humans. The Brazilian Amazon region has the highest number of arboviruses detected worldwide. In addition to arboviruses, malaria, caused by Plasmodium vivax, is endemic in the Amazon. Patients with malaria and arboviral disease frequently show similar clinical presentation and laboratory findings, making the diagnosis of the cause of the infection challenging. The aim of this study was to evaluate the potential for viral infections in patients with suspected malaria but without Plasmodium infection in the Brazilian Amazon. We recruited 200 subjects with suspected malaria in Manaus, Brazil. First, we tested for arboviruses in serum samples from 124 of the 200 participants using an arbovirus DNA microarray platform, which did not detect any virus. Then, we mixed the serum samples of the other 76 participants in 10 pools and subjected them to next-generation sequencing. Analysis of the sequencing data revealed the presence of only one arbovirus (Zika virus) in one sample pool. This analysis also detected the presence of primate erythroparvovirus 1 and pegivirus C. These results suggest that arboviruses are not the most frequent viral infections in patients with suspected malaria but without Plasmodium infection in the metropolitan region of Manaus. Implementation of specific viral surveillance tests will help in the early detection of viruses with epidemic potential.

Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients

Human pegivirus-1 (HPgV-1) is a lymphotropic human virus, typically considered nonpathogenic, but its infection can sometimes cause persistent viremia both in immunocompetent and immunosuppressed individuals. In a viral discovery research program in hematopoietic stem cell transplant (HSCT) pediatric patients, HPgV-1 was detected in 3 out of 14 patients (21.4%) using a target enrichment next-generation sequencing method, and the presence of the viruses was confirmed by agent-specific qRT-PCR assays. For the first time in this patient cohort, complete genomes of HPgV-1 were acquired and characterized. Phylogenetic analyses indicated that two patients had HPgV-1 genotype 2 and one had HPgV-1 genotype 3. Intra-host genomic variations were described and discussed. Our results highlight the necessity to screen HSCT patients and blood and stem cell donors to reduce the potential risk of HPgV-1 transmission.

Clinical and molecular aspects of human pegiviruses in the interaction host and infectious agent

Background

Human pegivirus 1 (HPgV-1) is a Positive-sense single-stranded RNA (+ ssRNA) virus, discovered in 1995 as a Flaviviridae member, and the closest human virus linked to HCV. In comparison to HCV, HPgV-1 seems to be lymphotropic and connected to the viral group that infects T and B lymphocytes. HPgV-1 infection is not persuasively correlated to any known human disease; nevertheless, multiple studies have reported a connection between chronic HPgV-1 infection and improved survival in HPgV-1/HIV co-infected patients with a delayed and favorable impact on HIV infection development. While the process has not been thoroughly clarified, different mechanisms for these observations have been proposed. HPgV-1 is categorized into seven genotypes and various subtypes. Infection with HPgV-1 is relatively common globally. It can be transferred parenterally, sexually, and through vertical ways, and thereby its co-infection with HIV and HCV is common. In most cases, the clearance of HPgV-1 from the body can be achieved by developing E2 antibodies after infection.

Main body

In this review, we thoroughly discuss the current knowledge and recent advances in understanding distinct epidemiological, molecular, and clinical aspects of HPgV-1.

Conclusion

Due to the unique characteristics of the HPgV-1, so advanced research on HPgV-1, particularly in light of HIV co-infection and other diseases, should be conducted to explore the essential mechanisms of HIV clearance and other viruses and thereby suggest novel strategies for viral therapy in the future.

Occurrence and molecular characterization of human pegivirus-1 (HPgV-1) viraemia in healthy volunteer blood donors from northern Portugal

Human Pegivirus-1 (HPgV-1) is a member of the Flaviviridae family and the Pegivirus genus. Despite having been discovered 25 years ago, there is still much to know regarding HPgV-1 clinical impact, as this virus is currently not associated with any pathology. Yet, HPgV-1 prevalence and molecular characterization is still unknown in many countries, including Portugal. To fill in this knowledge gap, this study aimed to determine the occurrence and molecular characterization of HPgV-1 in a group of healthy blood donors from the north of Portugal. Blood samples from 465 Portuguese blood donors were collected from a major Hospital Center in the north of Portugal. RNA was extracted and an initial nested RT-PCR was performed targeting the conserved 5'-UTR region of HPgV-1 genome. A second nested RT-PCR targeting the E2 region was performed for genotyping. Only one sample tested positive for HPgV-1 RNA, resulting in a prevalence of approximately 0.22%. Phylogenetic analyses confirmed the characterization as genotype 2, the most prevalent in Europe. This article is protected by copyright. All rights reserved.

METAVIROME COMPOSITION OF BRAZILIAN BLOOD DONORS POSITIVE FOR THE ROUTINELY TESTED BLOOD-BORNE INFECTIONS

Viral metagenomics is widely applied to characterize emerging viral pathogens but it can also reveal the virome composition in health and disease. The evaluation of the virome in healthy blood donors can provide important knowledge on possible transfusion threats. Currently, there is still a paucity of information regarding the virome of blood donors who test positive for routinely tested blood-borne infections. Such analysis may reveal co-infections which in turn appear to be crucial for transfusion medicine and for patient management. The aim of this study was to evaluate the metavirome in blood donors who tested positive for routinely tested blood-borne infections, the information for which is important for transfusion medicine and blood donor management. For this purpose, we analyzed 18 blood donations obtained from HIV and HBV-infected blood donors from the Brazilian Amazon (Amapa state) and 11 HIV, HBV, HCV, syphilis and Chagas disease - positive blood donations obtained from blood donors sampled in South Brazil (Rio Grande do Sul state). We additionally included a control group of 20 blood donors obtained from Southeast Brazil (State of São Paulo). Samples were assembled in pools and sequenced by the Illumina NovaSeq 6000 platform. To link a given virus with geographic region or type of blood donor, we performed supervised machine learning classification (fingerprint analysis). The virome of both locations was predominantly composed of commensal viruses. However, in HBV-infected blood donors from the Brazilian Amazon, the Human Pegivirus-1 (HPgV-1) reads were prevailing, while in HIV-infected donors from the same location, the torque teno virus (TTV) reads expressive abundance. In blood donors from South Brazil, the most abundant reads were classified as Human endogenous retrovirus K (HERV-K). Putative emerging viruses like the Human gemykibivirus-2 (HuGkV-2) were exclusively identified in samples from the Brazilian Amazon. The fingerprint analysis demonstrated that the HERV-K, TTV-7, 13, and 15 were statistically important for the infected blood donors, while TTV-5, 12 and 20 were linked to geographic localization. Our study revealed differences in the viral composition among blood donors who tested positive for routinely tested blood-borne infections from two different Brazilian regions and indicated the presence of putative emerging viruses in samples obtained from the Amazon. Together our results show that the presence of specific commensal viruses may be related donor infection status but additional investigations including larger study groups and samples from other Brazilian regions are needed to confirm this hypothesis.

Human pegivirus-1 infection in kidney transplant recipients: A single-center experience

Kidney transplantation is the treatment of choice for patients with end-stage renal disease. In the posttransplant period, the induced immunosuppression leads to an increased risk of developing infectious diseases, a leading cause of death after kidney transplantation. Human pegivirus-1 (HPgV-1) is considered a nonpathogenic human virus and is highly frequent in individuals parenterally exposed, however, its impact on kidney transplantation outcome is poorly understood. Given the scarcity of epidemiological data for this infection on organ recipients in Brazil, we conducted a study in a single center for kidney transplantation in Rio de Janeiro, aiming to determine HPgV-1 prevalence and genotypic distribution. Serum samples from 61 renal recipients, followed up for the first year after transplantation, were evaluated for viral RNA and genotypes were determined by sequencing of the 5'-untranslated region. HPgV-1 RNA was detected in 36.1% (22/61) of patients. Genotype 2 was the most commonly found (80.9%), followed by genotypes 3 (9.5%), 1, and 5, in 4.8% each. Statistical comparisons did not reveal any significant impact of HPgV-1 in patient outcome. Further epidemiologic studies are needed to understand if immunosuppression may interfere in HPgV-1 persistence rates and if viremia might impact graft dysfunction rates in kidney recipients.

Human pegivirus (HPgV, GBV-C) RNA in volunteer blood donors from a public hemotherapy service in Northern Brazil

Background

Human pegivirus (HPgV)—formerly known as GBV-C—is a member of the Flaviviridae family and belongs to the species Pegivirus C. It is a non-pathogenic virus and is transmitted among humans mainly through the exposure to contaminated blood and is often associated with human immunodeficiency virus (HIV) infection, among other viruses. This study aimed to determine the prevalence of HPgV viremia, its association with HIV and clinical epidemiological factors, as well as the full-length sequencing and genome characterization of HPgV recovered from blood donors of the HEMOPA Foundation in Belém-PA-Brazil.

Methods

Plasma samples were obtained from 459 donors, tested for the presence of HPgV RNA by the RT-qPCR. From these, a total of 26 RT-qPCR positive samples were submitted to the NGS sequencing approach in order to obtain the full genome. Genome characterization and phylogenetic analysis were conducted.

Results

The prevalence of HPgV was 12.42%. We observed the highest prevalences among donors aged between 18 and 30 years old (16.5%), with brown skin color (13.2%) and men (15.8%). The newly diagnosed HIV-1 prevalence was 26.67%. The HPgV genotype 2 (2a and 2b) was identified. No data on viral load value was found to corroborate the protective effect of HPgV on HIV evolution.

Conclusions

This study provided information regarding the HPgV infection among blood donors from HEMOPA Foundation. Furthermore, we genetically characterized the HPgV circulating strains and described by the first time nearly complete genomes of genotype 2 in Brazilian Amazon.

Low prevalence of human pegivirus 1 (HPgV-1) in HTLV-1 carriers from Belém, Pará, North Region of Brazil

Introduction

Human pegivirus 1 (HPgV-1) is a single-stranded, positive-sense RNA virus belonging to the Flaviviridae family with limited cause-effect evidence of the causation of human diseases. However, studies have shown a potential beneficial impact of HPgV-1 coinfection in HIV disease progression. Human T lymphotropic virus-1 (HTLV-1) is a retrovirus known for causing diseases, especially in muscle and white blood cells, in approximately 5% of patients. Thus, this study aimed to investigate the potential effects of an HPgV-1 infection in patients carrying HTLV-1 in the state of Pará in the North Region of Brazil.

Methods

A group of HTLV-1 carriers was compared to healthy controls. Blood samples were collected, data from medical regards were collected, and a questionnaire was administered. HPgV-1 and HTLV-1 positivity was determined by quantitative polymerase chain reaction (qRT-PCR). The data were analyzed to correlate the effects of HPgV-1 coinfection in HTLV-1 carriers.

Results

A total of 158 samples were included in the study: 74 HTLV-1-positive patients (46,8%) and 84 healthy controls (53,2%). The overall HPgV-1 positivity rate was 7.6% (12/158), resulting in a prevalence of 5.4% (4/74) and 9.5% (8/84) in HTLV-1 carriers and healthy controls, respectively. No significant differences were found when comparing any clinical or demographic data between groups.

Conclusion

This study indicated that the prevalence of HPgV-1 infection is low in HTLV-1 carriers in Belém, Pará, and probably does not alter the clinical course of HTLV-1 infection, however, further studies are still needed.

Global prevalence of human pegivirus-1 in healthy volunteer blood donors: a systematic review and meta-analysis

BACKGROUND AND OBJECTIVES

The local prevalence of HPgV-1 has been reported from different countries worldwide, but the global prevalence of HPgV-1 remains unknown. The aim of this systematic review and meta-analysis was to gather data from the literature to estimate the prevalence of HPgV-1 in healthy volunteer blood donors in the world.

MATERIALS AND METHODS

We searched PubMed, EMBASE, Scopus and Google Scholar databases for records up to January 2019 and included studies reporting HPgV-1 virus prevalence amongst healthy volunteer blood donors based on the detection of HPgV-1 RNA.

RESULTS

In all, we included 79 studies for the systematic review and 63 for the meta-analysis. Based on the random effect meta-analysis of 35 468 volunteer blood donors, we found the global prevalence of HPgV-1 to be 3·1% (95% CI, 2·4-4·1). The pooled prevalences of HPgV-1 were 1·7% (95% CI, 1·1-2·6) in North America, 9·1% (95% CI, 6·4-12·7) in South America, 2·3% (95% CI, 2%, 2·8) in Europe and 2·4% (95% CI, 1·4-4) in Asia. Subgroup analyses based on age, gender or risk factors were not possible.

CONCLUSION

Approximately 3 in 100 blood donations worldwide are positive for HPgV-1 increasing the risk of infection from transfusion of their components to subsequent recipients. Further research on virus pathogenicity is required before recommending routine screening of HPgV-1 for healthy volunteer blood donors.

Molecular and Clinical Profiles of Human Pegivirus Type 1 Infection in Individuals Living with HIV-1 in the Extreme South of Brazil

Human pegivirus type 1 (HPgV-1) infection has been associated with a beneficial effect on the prognosis of human immunodeficiency virus type 1 (HIV-1)-coinfected individuals. However, the mechanisms involved in this protection are not yet fully elucidated. To date, circulating HPgV-1 genotypes in HIV-1-infected individuals have not yet been identified in the extreme south of Brazil. The present study aimed to determine the genotypic circulation of HPgV-1 and the influence of HPgV-1 status and persistence time on the evolution of HIV-1 infection. A retrospective cohort of 110 coinfected individuals was analyzed. Samples were subjected to viral RNA extraction, cDNA synthesis, nested PCR, and genotyping. Genotypes 1 (2.8%), 2 (47.9% of subtype 2a and 42.3% of subtype 2b), and 3 (7%) were identified. In antiretroviral treatment-naïve subjects HPgV-1 subtype 2b was associated with lower HIV-1 viral load (VL) rates (p = 0.04) and higher CD4+ T-cell counts (p = 0.03) than was subtype 2a, and the positivity for HPgV-1 was associated with higher CD4+ T-cell counts (p = 0.02). However, there was no significant difference in HIV-1 VL between HPgV-1-positive and HPgV-1-negative subjects (p = 0.08). There was no significant association between the different groups in HPgV-1 persistence and median HIV-1 VL (p = 0.66) or CD4+ T-cell counts (p = 0.15). HPgV-1 subtype 2b is associated with better prognosis of HIV-1 infection. Although HPgV-1 infection is persistent, our data suggest that the time of infection does not influence HIV-1 VL or CD4+ T-cell counts in coinfected subjects.