The plasma virome of febrile adult Kenyans shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus)

Abstract

Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75 %), pegivirus C (GBV-C) (67 %), alpha anellovirus (59 %), gamma anellovirus (55 %), beta anellovirus (41 %), dengue virus genotype 2 (DENV-2) (16 %), human immunodeficiency virus type 1 (6 %), human herpesvirus 6 (6 %), HBV (4 %), rotavirus (4 %), hepatitis B virus (4 %), rhinovirus C (2 %), Merkel cell polyomavirus (MCPyV; 2 %) and Kadipiro virus (2 %). Ranking by overall percentage of viral reads yielded similar results. Characterization of viral nucleic acids in the plasma of a febrile East African population showed a high frequency of parvovirus B19 and DENV infections and detected a reovirus (Kadipiro virus) previously reported only in Asian Culex mosquitoes, providing a baseline to compare with future virome studies to detect emerging viruses in this region.

Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host–microbe interactions

“…S2). More importantly, two recent analyses of the human fecal virome have identified DNA sequences belonging to LCDV-1 and SGIV (30,31), and LCDV-1 has also been identified in the sequences of circulating DNAs in human blood (32,33).…”

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

“…Overall, DicV presence did not vary significantly among the 3 major sub-cohorts of fever without source , the Human blood-associated dicistrovirus sequence reported from a Peruvian patients with fever of unknown aetiology [21], and the KENYA sequence detected by our retrospective analysis in one pool (SRR4255933) from a study that investigated the plasma virome of febrile adult Kenyans [22]. (c) Phylogenetic tree of the capsid region of DicV.…”

“…In comparison to the Tanzanian sequences, the Peruvian DicV viral sequence showed amino acid identities as low as 35.5% and 22% in the RdRp and the capsid regions, respectively, confirming that they belong to different genera (Figure 2b,c). Finally, when analysing publicly available sequence databases from a recent study that investigated the plasma virome of febrile adult Kenyans [22], and thus has absolutely no link with our investigations, we identified 2'290 DicV reads covering 96.1% (5'350 nt) of ORF1 and 97.5% (2'525 nt) of ORF2 in one pool (SRR4255933). For ORF1, the covered sequence showed 95.4-96.4% nucleotide identity and 98.9-99.2% amino acid identity compared to the Tanzanian DicV sequences.…”

The clinical use of parvovirus B19 assays: recent advances

“…Next generation sequencing methodologies are increasingly applied to investigation of clinical samples, and metagenomic investigations can be aimed at the identification of viral sequences in either blood or solid tissues. B19V genomic sequences have been detected in blood as part of the plasma virome in normal population [31], in peculiar epidemiological and clinical contexts [105], or in situations with underlying pathological process in the quest for etiological infectious agents [106][107][108]. This kind of experimental evidence is only now becoming to accumulate and will likely provide valuable information on the presence and relevance of B19V in many pathological processes.…”