Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs

Abstract

Background-Next-generation metagenomic sequencing (NGMS) has opened new frontiers in microbial discovery but has been clinically characterized in only a few settings. Objective-To explore the plasma virome of persons who inject drugs while characterizing the sensitivity and accuracy of NGMS compared to quantitative clinical standards. Design-Longitudinal and cross-sectional studies. Participants-Hepatitis C virus (HCV) and human immunodeficiency virus (HIV) co-infected persons enrolled in a clinical trial (NCT01285050) and/or a well-characterized cohort study of persons who have injected drugs. Measurements-Viral nucleic acid in plasma by NGMS and quantitative polymerase chain reaction (PCR). Results-NGMS generated a total of 600 million reads, which included the expected HIV and HCV RNA sequences. HIV and HCV reads were consistently identified only when samples contained >10,000 copies or IU/ml as determined by quantitative PCR. A novel RNA virus, human hepegivirus-1 (HHpgV-1) was also detected by NGMS in 4 samples from 2 persons in the clinical trial. Because of this unexpected finding, using a quantitative PCR assay for HHpgV-1, infection was also detected in 17 (10.9%) of 156 members of a cohort of persons who injected drugs in whom HHpgV-1 viremia persisted for a median of at least 4538 days and was associated with detection of other bloodborne viruses such as HCV RNA and SEN virus D Limitations-The medical importance of HHpgV-1infection remains unknown.

Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases

“…This compares to 10 4-5 CFU/mL for detection of pathogens by special stains directly from a specimen (ie, Gram stain), 10 2-3 CFU/mL for growth in culture, and 10-100 CFU/mL for nucleic acid amplification-based methods [31]. It also varies by specimen type, as the limit of detection of mNGS for hepatitis C virus and HIV from plasma has been reported as high as 1 × 10 4 copies/mL, as determined by quantitative PCR [32]. Use of an internal control is extremely important to identify analytic failures and specimens with unusual cellularity that may result in reduced analytical sensitivity.…”

Hepatitis C virus surveillance and identification of human pegivirus 2 in a large Cameroonian cohort

“…10 The sequence identities of the Cameroonian HPgV-2 strains compared to this US strain (91.3%, K4583; 96%, D2931) and to others overall (93%, K8543; 94%, D2931) are consistent with previous reports. [9][10][11][12]14,16 HPgV-2 infections were not restricted to a single site in our study; rather, a total of 9 collection sites had specimens that were seropositive for HPgV-2, suggesting that the prevalence reported here is not due to a location-specific outbreak ( Figure S1).…”

“…Notably, both of the viremic HPgV-2 infections identified in Cameroon were co-infected with HCV and HIV, consistent with previous reports of higher rates of HPgV-2 viremia within HCV/ HIV-positive cohorts (3.5%, China; 10.9% USA). 12,14 The strains identified in Cameroon are most closely related to a US strain with two serial bleeds from a single individual (ABT0035P/ABT0041P). 10 The sequence identities of the Cameroonian HPgV-2 strains compared to this US strain (91.3%, K4583; 96%, D2931) and to others overall (93%, K8543; 94%, D2931) are consistent with previous reports.…”

“…Since HPgV-2 screening was limited to HCV RNA-positive specimens, the prevalence of HPgV-2 in HCV-negative populations of Cameroon is unknown. While previous studies have primarily identified viremic HPgV-2 infections in HCV co-infected individuals, [10][11][12][13][14][15] the role of HCV co-infection in the persistence of HPgV-2 viremia remains unknown. Likewise, additional studies are necessary to determine whether HPgV-2 impacts human health, and screening in additional geographical locations may identify previously underappreciated diversity amongst HPgV-2 strains.…”

“…Although a direct measurement has not been made in Cameroon, a prediction model estimates the prevalence of HCV RNA in Cameroon to be 0.7%, 7 which is similar to the rate of 0.9% (95% CI: 0.3%-1.6%) recently observed in the neighbouring Democratic Republic of the Congo. 8 Human pegivirus 2 (HPgV-2) is a newly identified virus that is most closely related to rodent and bat pegiviruses, sharing <32% amino acid identity with these relatives, 9,10 HPgV-2 infections have been identified in plasma specimens from the USA, UK, Germany, Iran and China, [9][10][11][12][13][14][15][16] indicating that this virus is already present on at least 3 continents. The expansion of HPgV-2 surveillance to additional parts of the world will determine the prevalence and extent of genetic diversity of HPgV-2.…”