Characterization of genetically diverse HIV type 1 from a London cohort: near full-length genomic analysis of a subtype H strain.
HIV-1 is characterized by an exceptional level of sequence diversity and a rapid rate of evolution. HIV diversity has implications for reliability of assays designed to detect and monitor infection, pathogenesis, disease progression, response to antiviral therapeutics, resistance pathways, and vaccine development. In the present study, HIV-1 strain diversity was assessed for a small clinical cohort (n = 15) from London, England at risk for infection with non-subtype B strains. Analysis of gag p24, pol IN, and env gp41 IDR revealed the presence of five subtypes (A, B, C, D, H), CRF02_AG, and four unique recombinant forms. Due to the paucity of complete subtype H genomes available, we performed near full-length genome sequence analysis on the candidate subtype H strain, designated as 00GB.AC4001. Phylogenetic analysis revealed that it formed a monophyletic cluster with the three available subtype H reference sequences. Bootscanning analysis confirmed that 00GB.AC4001 represents a new nonrecombinant subtype H genome.
Holzmayer
Vera
V
Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, USA.
Aitken
Celia
C
Skinner
Celia
C
Ryall
Laura
L
Devare
Sushil G
SG
Hackett
John
J
D015331:Cohort Studies; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D015700:HIV Envelope Protein gp41 / Q000032:analysis / Q000235:genetics; D015658:HIV Infections / Q000097:blood / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008131:London; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000032:analysis / Q000097:blood / Q000235:genetics; D017422:Sequence Analysis, DNA; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000032:analysis / Q000235:genetics; D054302:pol Gene Products, Human Immunodeficiency Virus / Q000032:analysis / Q000235:genetics
D015700:HIV Envelope Protein gp41; D012367:RNA, Viral; D054301:gag Gene Products, Human Immunodeficiency Virus; D054302:pol Gene Products, Human Immunodeficiency Virus