title: High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.
abstract: Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this diversity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of sampling and/or experimental methods that do not fully account for errors generated through amplification and sequencing of viral RNAs. We investigated the extent and pattern of genetic diversity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma samples (n = 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from amplification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence diversities of viral populations were very low, with conservative estimates of the average levels of genetic diversity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some samples suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic diversity and disease severity, immune status, or level of viremia.
authors.affiliation: Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. khoat@oucru.org
authors.forename: Khoa T D
authors.initials: KT
authors.lastname: Thai
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Henn
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
authors.forename: Vianney
authors.initials: V
authors.lastname: Tricou
authors.forename: Nguyen Minh
authors.initials: NM
authors.lastname: Nguyet
authors.forename: Patrick
authors.initials: P
authors.lastname: Charlebois
authors.forename: Niall J
authors.initials: NJ
authors.lastname: Lennon
authors.forename: Lisa
authors.initials: L
authors.lastname: Green
authors.forename: Peter J
authors.initials: PJ
authors.lastname: de Vries
authors.forename: Tran Tinh
authors.initials: TT
authors.lastname: Hien
authors.forename: Jeremy
authors.initials: J
authors.lastname: Farrar
authors.forename: H Rogier
authors.initials: HR
authors.lastname: van Doorn
authors.forename: Menno D
authors.initials: MD
authors.lastname: de Jong
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.forename: Cameron P
authors.initials: CP
authors.lastname: Simmons
mesh_terms: D000293:Adolescent; D000328:Adult; D001483:Base Sequence; D060085:Coinfection / Q000821:virology*; D003715:Dengue / Q000821:virology*; D003716:Dengue Virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D014759:Viral Envelope Proteins / Q000235:genetics / Q000378:metabolism; D055815:Young Adult
chemical_list: D014759:Viral Envelope Proteins
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