title: HIV type 1 mutational patterns in HIV type 1 subtype C-infected long-term survivors in Karonga District Malawi: further analysis and correction.
abstract: Here we present new sequence data from HIV-1 subtype C-infected long-term survivors (LTS) from Karonga District, Malawi. Gag and env sequence data were produced from nine individuals each of whom has been HIV-1 positive for more than 20 years. We show that the three amino acid deletion in gag p17 previously described from these LTS is not real and was a result of an alignment error. We find that the use of dried blood spots for DNA-based studies is limited after storage for 20 years. We also show some unlikely amino acid changes in env C2-V3 in LTS over time and different patterns of genetic divergence among LTS. Although no clear association between mutations and survival could be shown, amino acid changes that are present in more than one LTS may, in the future, be shown to be important.
authors.affiliation: Molecular Evolution and Systematics Laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland, Galway, Ireland.
authors.forename: Ishla
authors.initials: I
authors.lastname: Seager
authors.forename: Michael D
authors.initials: MD
authors.lastname: Leeson
authors.forename: Amelia C
authors.initials: AC
authors.lastname: Crampin
authors.forename: Dominic
authors.initials: D
authors.lastname: Mulawa
authors.forename: Neil
authors.initials: N
authors.lastname: French
authors.forename: Judith R
authors.initials: JR
authors.lastname: Glynn
authors.forename: Simon A A
authors.initials: SA
authors.lastname: Travers
authors.forename: Grace P
authors.initials: GP
authors.lastname: McCormack
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D005260:Female; D015752:Genes, env / Q000235:genetics*; D015488:HIV Antigens / Q000235:genetics*; D020276:HIV Long-Term Survivors / Q000706:statistics & numerical data*; D006679:HIV Seropositivity / Q000453:epidemiology / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008295:Malawi / Q000453:epidemiology; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017384:Sequence Deletion / Q000235:genetics; D054301:gag Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D015488:HIV Antigens; D054301:gag Gene Products, Human Immunodeficiency Virus; C054858:p17 protein, Human Immunodeficiency Virus Type 1