Metagenomic identification of human Gemykibivirus-2 (HuGkV-2) in parenterally infected blood donors from the Brazilian Amazon

Bezerra, Rafael Santos; Bitencourt, Hellen Tayaná; Covas, Dimas Tadeu; Kashima, Simone; Slavov, Svetoslav Nanev

doi:10.1016/j.ijid.2020.06.096

Cited by 9 publications

(7 citation statements)

References 10 publications

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“…MH734253). GemyCV-SL1 has been detected in various human samples [ 27 , 28 , 29 , 30 ], including sterile sites such as cerebral spinal fluid, but the clinical significance of the virus infection is not established. To date, only one case study of a patient with respiratory distress provided evidence for the virus being the causative agent of disease [ 29 ].…”

Section: Resultsmentioning

confidence: 99%

Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

Fomsgaard

Tahas

Spieß

et al. 2023

Viruses

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Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human–animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.

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Section: Resultsmentioning

confidence: 99%

Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

Fomsgaard

Tahas

Spieß

et al. 2023

Viruses

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“…Gemykibivirus belongs to a divergent group of single-stranded DNA viruses, and it was detected in some MSM with or without HIV-1 infection. Several studies showed its presence/enrichment in HIV-1infected people and also patients with other diseases (30)(31)(32)(33), which suggested this virus could be associated with human disease (34). Even though more evidence is still needed, the detection of gemykibivirus here raises question about its pathogenic role in human.…”

Section: Discussionmentioning

confidence: 98%

HIV-1 Infection Alters the Viral Composition of Plasma in Men Who Have Sex with Men

et al. 2021

mSphere

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Altered gut virome and expanded abundance of certain viruses were found in HIV-1-infected individuals. It remains largely unknown how plasma virus composition changes during HIV-1 infection and antiretroviral therapy (ART). We performed viral metagenomic analysis on viral particles enriched from human plasma from 101 men who have sex with men (MSM) with or without HIV-1 infection and whether or not on ART and compared the differences in the plasma virome. An increased plasma viral abundance of main eukaryotic viruses was observed during HIV-1 infection in MSM, especially in AIDS patients (CD4+ T cell counts of <200). Anellovirus, pegivirus and hepatitis B virus (HBV) were the most abundant blood-borne viruses detected among MSM and HIV-1-infected individuals, and anellovirus and pegivirus were closely related to HIV-1 infection. High diversity of anelloviruses was found mostly in HIV-1-infected MSM, and their abundance was positively correlated with the HIV-1 viral load, but negatively correlated with both CD4+ T cell counts and CD4+/CD8+ ratio; in contrast, the abundance of pegivirus showed opposite correlations. ART usage could restore the plasma virome toward that of HIV-1-negative individuals. These data showed an expansion in abundance of certain viruses during HIV-1 infection, indicating the higher risk of shedding some blood-borne viruses in these individuals. These investigations indicate that both anellovirus and pegivirus may play certain roles in HIV disease progression. IMPORTANCE Though an increasing number of studies have indicated the existence of an interaction between the virome and human health or disease, the specific role of these plasma viral components remains largely unsolved. We provide evidence here that an altered plasma virome profile is associated with different immune status of HIV-1 infection. Specific resident viruses, such as anellovirus and pegivirus, may directly or indirectly participate in the disease progression of HIV-1 infection. These results can help to determine their clinical relevance and design potential therapies.

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“…The swift progress of next-generation sequencing (NGS) technology coupled with metagenomics has proven adept at unveiling a spectrum of novel circular ssDNA viruses encoding the Rep protein (Circular Rep-encoding Single-Stranded DNA) or RNA viruses [9]. These advancements extend across various specimen categories, encompassing fecal samples [10], heterogeneous mixtures [11], human subjects [12][13][14], bat populations [15], turtles [16], avian species [17], insects [18,19], plants [20], parasites [21,22], and environmental matrices [23]. This technological synergy facilitates the isolation and comprehensive characterization of viral diversity within diverse ecosystems.…”

Section: Introductionmentioning

confidence: 99%

Genomoviruses in Liver Samples of Molossus molossus Bats

Couto,

Abreu,

Rodrigues

et al. 2024

Microorganisms

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CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses’ impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.

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Metagenomic identification of human Gemykibivirus-2 (HuGkV-2) in parenterally infected blood donors from the Brazilian Amazon

Cited by 9 publications

References 10 publications

Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

HIV-1 Infection Alters the Viral Composition of Plasma in Men Who Have Sex with Men

Genomoviruses in Liver Samples of Molossus molossus Bats

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