Structural defects and variations in the HIV-1 nef gene from rapid, slow and non-progressor children.
OBJECTIVE
Evaluation of sequence evolution as well as structural defects and mutations of the human immunodeficiency virus-type 1 (HIV-1) nef gene in relation to disease progression in infected children.


METHODS
We examined a large number of nef alleles sequentially derived from perinatally HIV-1-infected children with different rates of disease progression: six non-progressors (NPs), four rapid progressors (RPs), and three slow progressors (SPs).


METHODS
Nef alleles (182 total) were isolated from patients' peripheral blood mononuclear cells (PBMCs), sequenced and analysed for their evolutionary pattern, frequency of mutations and occurrence of amino acid variations associated with different stages of disease.


RESULTS
The evolution rate of the nef gene apparently correlated with CD4+ decline in all progression groups. Evidence for rapid viral turnover and positive selection for changes were found only in two SPs and two RPs respectively. In NPs, a higher proportion of disrupted sequences and mutations at various functional motifs were observed. Furthermore, NP-derived Nef proteins were often changed at residues localized in the folded core domain at cytotoxic T lymphocytes (CTL) epitopes (E(105), K(106), E(110), Y(132), K(164), and R(200)), while other residues outside the core domain are more often changed in RPs (A(43)) and SPs (N(173) and Y(214)).


CONCLUSIONS
Our results suggest a link between nef gene functions and the progression rate in HIV-1-infected children. Moreover, non-progressor-associated variations in the core domain of Nef, together with the genetic analysis, suggest that nef gene evolution is shaped by an effective immune system in these patients.
Casartelli
Nicoletta
N
Division of Immunology and Infectious Disease, Children's Hospital 'Bambino Gesù', Rome, Italy.
Di Matteo
Gigliola
G
Argentini
Claudio
C
Cancrini
Caterina
C
Bernardi
Stefania
S
Castelli
Guido
G
Scarlatti
Gabriella
G
Plebani
Anna
A
Rossi
Paolo
P
Doria
Margherita
M
D000293:Adolescent; D000483:Alleles; D000595:Amino Acid Sequence; D018791:CD4 Lymphocyte Count; D015496:CD4-Positive T-Lymphocytes / Q000473:pathology; D002648:Child; D002675:Child, Preschool; D018450:Disease Progression; D000939:Epitopes / Q000235:genetics; D019143:Evolution, Molecular; D015693:Gene Products, nef / Q000235:genetics; D015754:Genes, nef; D015658:HIV Infections / Q000276:immunology* / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D016415:Sequence Alignment; D013602:T-Lymphocytes, Cytotoxic / Q000276:immunology; D014758:Viral Core Proteins / Q000235:genetics; D054311:nef Gene Products, Human Immunodeficiency Virus
D000939:Epitopes; D015693:Gene Products, nef; D014758:Viral Core Proteins; D054311:nef Gene Products, Human Immunodeficiency Virus