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

Carolyne N. Ngoi,Eric Delwart,Xutao Deng,Matt A. Price,Juliana Siqueira,Eduard J. Sanders,Linlin Li,Susan M. Graham,Peter Mugo

doi:10.1099/jgv.0.000644

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.

Highlights

Cryopreserved samples from patients with unexplained fever can be used for emerging virus surveillance
To describe the plasma virome and identify emerging viruses in a population of adults with unexplained fever from East Africa, we enriched, sequenced, and identified viral nucleic acids from 498 febrile adults enrolled in a study of acute human immunodeficiency virus type 1 (HIV-1) infection (AHI) at two sites in coastal Kenya
The raw sequence data for each pool is available at the National Center for Biotechnology Information (NCBI) Short Read Archive under GenBank accession number SRP090133

Summary

Introduction

Cryopreserved samples from patients with unexplained fever can be used for emerging virus surveillance. Enrichment of viral nucleic acids followed by random nucleic acid amplification, deep DNA sequencing, and similarity searches to all previously sequenced viral genomes or proteomes have each been used to identify known and previously uncharacterized ‘new’ viral genomes. Such viral metagenomics approaches were pioneered in 2001 using mammalian samples (Allander et al, 2001) and in 2002 with environmental samples (Breitbart et al, 2002). To describe the plasma virome and identify emerging viruses in a population of adults with unexplained fever from East Africa, we enriched, sequenced, and identified viral nucleic acids from 498 febrile adults enrolled in a study of acute human immunodeficiency virus type 1 (HIV-1) infection (AHI) at two sites in coastal Kenya

Methods

Results

Conclusion