- Email: [email protected]
AIDS: the evolving story
COMMENT
AIDS: the evolving story Rodney E. Phillips, Annette Oxenius, David A. Price and Charles R.M. Bangham
A
major aim in the study of immune responses to AIDSassociated retroviruses is to define how viral replication is controlled during the long course of infection. In early studies of HIV immunity, virus-specific CD81 cytotoxic T lymphocyte (CTL) responses were readily detected1,2. Over the past decade, increasing evidence has been generated to suggest that these lymphocytes play a crucial role in containing HIV replication. Activated HIVspecific CTLs emerge early in infection, coincident with a decline in the initial viraemia, and remain abundant throughout chronic infection until the rapid rise in viral load at the onset of AIDS (Ref. 3). The central role of CTLs in virus control is illustrated by the simian model of AIDS, in which total CD81-T-cell depletion results in a clear rise in viraemia, whereas the return of antigen-specific CTLs is closely followed by suppression of viraemia4,5. Furthermore, in crosssectional human studies, levels of HIV-specific CTLs are negatively correlated with viraemia6. These studies imply that viruses that persist in the presence of ongoing CTL activity must have immune evasion properties. Viral variation High viral replication rates, in association with error-prone retroviral reverse transcription7, combine to generate a genetically diverse viral population within immunodeficiency-virus-infected individuals8. These quasispecies are subject to selection pressures, such as immune responses and anti-retroviral drug therapy, within infected individuals9–11. If the host CTLs constitute a significant anti-retroviral force, then variant viruses that evade this response should possess an evolutionary advantage12. Studies
in acute primary HIV-1 infection have clearly demonstrated positive selection for CTL ‘escape’ mutations13,14. Additionally, viruses that escape CTL recognition can accumulate in the later stages of infection15, and adoptive transfer of large numbers of monospecific CTLs can skew the viral population in favour of escape variants16. However, the role of CTLmediated selection of virus variants during the chronic phase of infection has remained controversial17. An elegant new analysis using the SIV model of AIDS has provided further experimental evidence supporting the CTL escape hypothesis18. Five rhesus macaques sharing some, but not all, major histocompatibility complex (MHC) class I molecules, and matched at MHC class II loci, were infected with an identical inoculum of SIV. Three animals had detectable CTLs directed towards antigens in the viral Env and Nef proteins. Sequence analysis of plasma virion RNA taken up to 889 days after infection of these three macaques revealed the accumulation of amino acid substitutions in several targeted MHC class I-restricted epitope regions, which were initially recognized by CTLs. The vast majority of variant epitopes had diminished immunogenicity either owing to failure of MHC class I binding or to impaired recognition by autologous CTLs. R.E. Phillips*, A. Oxenius and D.A. Price are in the University of Oxford, Nuffield Dept of Clinical Medicine, The John Radcliffe Hospital, Level 7, Oxford, UK OX3 9DU; C.R.M. Bangham is in the Imperial College of Science, Technology and Medicine, St Mary’s Campus, Norfolk Place, London, UK W2 1PG. *tel: 144 1865 221478, fax: 144 1865 220993, e-mail: [email protected]
0966-842X/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved. TRENDS
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Selection and sequence analysis How can positive selection be inferred from nucleotide sequence analysis? It is very difficult to make precise measurements of the fitness of different HIV-1 clones in vivo (i.e. their net replication rate under different physiological conditions). An established technique to identify positive selection is to measure the relative frequencies of non-synonymous (coding) nucleotide changes and synonymous (non-coding) nucleotide changes amongst a selection of viral clones, normalized to the proportion of redundant nucleotide residues in the coding sequence. A widely used index is the dN/dS (non-synonymous/synonymous) ratio, defined by Nei and Gojobori19. Such an analysis was applied in the study by Evans et al.18 and revealed clear evidence of positive selection focussed at the CTL epitope-encoding regions in the plasma virion RNA in three macaques. The lack of positive selection for amino acid substitutions in regions of the viral genome containing MHCmismatched CTL epitopes within the same individual, and in corresponding regions of the virus in MHC-mismatched individuals, provided important internal and external controls. Directly comparable results have been previously reported in HIV-1 infection13. The data of Evans et al. also revealed co-evolution of variant sequences on the same RNA strand, providing unequivocal evidence that individual viruses can acquire multiple escape epitopes. This last finding is important, as an evolutionary model of viral escape would predict that single virions should adapt in this way. The work of Evans et al. provides further strong support for the idea that CTLs control immunodeficiency viruses, and that the PII: S0966-842X(00)01706-6
NO. 4
APRIL 2000
COMMENT
selective pressure they exert moulds the viral population during persistent infection. Additionally, this study corroborates earlier work15,16 linking progressive disease with the accumulation of serial escape mutations and thus with loss of CTL control. These data provide a plausible explanation for two observations: the correlation between human leukocyte antigen (HLA) class I homozygosity and accelerated disease progression; and the protective effect of class I heterozygosity20,21. However, uncertainties remain concerning the crucial interactions between HIV and the immune response during the very long period of containment characteristic of chronic viral infection. The simian model does not mimic this part of the disease process precisely, and further human studies are therefore required to address these issues in detail. References 1 Plata, F. et al. (1987) AIDS virus-specific cytotoxic T lymphocytes in lung disorders. Nature 328, 348–351 2 Walker, B.D. et al. (1987) HIV-specific cytotoxic T lymphocytes in seropositive individuals. Nature 328, 345–348 3 Goulder, P. et al. (1997) Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses. Immunol. Rev. 159, 17–29
4 Jin, X. et al. (1999) Dramatic rise in plasma viremia after CD81 T cell depletion in simian immunodeficiency virus-infected macaques. J. Exp. Med. 189, 991–998 5 Schmitz, J.E. et al. (1999) Control of viremia in simian immunodeficiency virus infection by CD81 lymphocytes. Science 283, 857–860 6 Ogg, G.S. et al. (1998) Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA. Science 279, 2103–2106 7 Roberts, J.D. et al. (1988) The accuracy of reverse transcriptase from HIV-1. Science 242, 1171–1173 8 Goodenow, M. et al. (1989) HIV-1 isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions. J. Acquired Immune Defic. Syndr. 2, 344–352 9 Wolinsky, S.M. et al. (1996) Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272, 537–542 10 Harrigan, P.R. and Alexander, C.S. (1999) Selection of drug-resistant HIV. Trends Microbiol. 7, 120–123 11 Harrigan, P.R. and Alexander, C.S. (1999) Selection of drug-resistant HIV: Erratum. Trends Microbiol. 7, 302 12 Phillips, R.E. et al. (1991) Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature 354, 453–459 13 Price, D.A. et al. (1997) Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc. Natl. Acad. Sci. U. S. A. 94, 1890–1895 14 Borrow, P. et al. (1997) Antiviral pressure exerted by HIV-1-specific
15
16
17
18
19
20
21
cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat. Med. 3, 205–211 Goulder, P.J. et al. (1997) Late escape from an immunodominant cytotoxic Tlymphocyte response associated with progression to AIDS. Nat. Med. 3, 212–217 Koenig, S. et al. (1995) Transfer of HIV1-specific cytotoxic T lymphocytes to an AIDS patient leads to selection for mutant HIV variants and subsequent disease progression. Nat. Med. 1, 330–336 Brander, C. et al. (1998) Lack of strong immune selection pressure by the immunodominant, HLA- A*0201restricted cytotoxic T lymphocyte response in chronic human immunodeficiency virus-1 infection. J. Clin. Invest. 101, 2559–2566 Evans, D.T. et al. (1999) Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nat. Med. 5, 1270–1276 Nei, M. and Gojobori, T. (1986) Simple methods for estimating the numbers of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426 Tang, J. et al. (1999) HLA class I homozygosity accelerates disease progression in human immunodeficiency virus type 1 infection. AIDS Res. Hum. Retroviruses 15, 317–324 Carrington, M. et al. (1999) HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 283, 1748–1752
Sortase: the surface protein anchoring transpeptidase and the LPXTG motif Richard P. Novick
N
ot so very long ago, staphylococci were considered to be ‘bald’ as they are non-motile and lack macroscopic surface appendages such as the pili or fimbriae found on many bacilli. Although surface appendages remain inapparent, electron microscopy has revealed that, rather than being bald, the organism is a fuzzy ball, being decorated with a myriad of filamentous
proteins that cover essentially the entire visible surface area and, moreover, are rather stably
R.P. Novick is in the Program in Molecular Pathogenesis, Skirball Institute, Depts of Microbiology and Medicine, New York University Medical School, New York, NY 10016, USA. tel: 11 212 263 6290, fax: 11 212 263 8951, e-mail: [email protected]
0966-842X/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved. TRENDS
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MICROBIOLOGY
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attached. Surface proteins, also found on most other Gram-positive bacteria, have major roles in the interactions of the microorganism with its environment and particularly with the animal host, where they serve as agglutinins and adhesins, block phagocytosis and prevent opsonization. The mechanisms of their export and attachment are therefore of considerable significance for the overall PII: S0966-842X(00)01741-8
NO. 4
APRIL 2000
AIDS: the evolving story Rodney E. Phillips, Annette Oxenius, David A. Price and Charles R.M. Bangham
A
major aim in the study of immune responses to AIDSassociated retroviruses is to define how viral replication is controlled during the long course of infection. In early studies of HIV immunity, virus-specific CD81 cytotoxic T lymphocyte (CTL) responses were readily detected1,2. Over the past decade, increasing evidence has been generated to suggest that these lymphocytes play a crucial role in containing HIV replication. Activated HIVspecific CTLs emerge early in infection, coincident with a decline in the initial viraemia, and remain abundant throughout chronic infection until the rapid rise in viral load at the onset of AIDS (Ref. 3). The central role of CTLs in virus control is illustrated by the simian model of AIDS, in which total CD81-T-cell depletion results in a clear rise in viraemia, whereas the return of antigen-specific CTLs is closely followed by suppression of viraemia4,5. Furthermore, in crosssectional human studies, levels of HIV-specific CTLs are negatively correlated with viraemia6. These studies imply that viruses that persist in the presence of ongoing CTL activity must have immune evasion properties. Viral variation High viral replication rates, in association with error-prone retroviral reverse transcription7, combine to generate a genetically diverse viral population within immunodeficiency-virus-infected individuals8. These quasispecies are subject to selection pressures, such as immune responses and anti-retroviral drug therapy, within infected individuals9–11. If the host CTLs constitute a significant anti-retroviral force, then variant viruses that evade this response should possess an evolutionary advantage12. Studies
in acute primary HIV-1 infection have clearly demonstrated positive selection for CTL ‘escape’ mutations13,14. Additionally, viruses that escape CTL recognition can accumulate in the later stages of infection15, and adoptive transfer of large numbers of monospecific CTLs can skew the viral population in favour of escape variants16. However, the role of CTLmediated selection of virus variants during the chronic phase of infection has remained controversial17. An elegant new analysis using the SIV model of AIDS has provided further experimental evidence supporting the CTL escape hypothesis18. Five rhesus macaques sharing some, but not all, major histocompatibility complex (MHC) class I molecules, and matched at MHC class II loci, were infected with an identical inoculum of SIV. Three animals had detectable CTLs directed towards antigens in the viral Env and Nef proteins. Sequence analysis of plasma virion RNA taken up to 889 days after infection of these three macaques revealed the accumulation of amino acid substitutions in several targeted MHC class I-restricted epitope regions, which were initially recognized by CTLs. The vast majority of variant epitopes had diminished immunogenicity either owing to failure of MHC class I binding or to impaired recognition by autologous CTLs. R.E. Phillips*, A. Oxenius and D.A. Price are in the University of Oxford, Nuffield Dept of Clinical Medicine, The John Radcliffe Hospital, Level 7, Oxford, UK OX3 9DU; C.R.M. Bangham is in the Imperial College of Science, Technology and Medicine, St Mary’s Campus, Norfolk Place, London, UK W2 1PG. *tel: 144 1865 221478, fax: 144 1865 220993, e-mail: [email protected]
0966-842X/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved. TRENDS
IN
MICROBIOLOGY
147
VOL. 8
Selection and sequence analysis How can positive selection be inferred from nucleotide sequence analysis? It is very difficult to make precise measurements of the fitness of different HIV-1 clones in vivo (i.e. their net replication rate under different physiological conditions). An established technique to identify positive selection is to measure the relative frequencies of non-synonymous (coding) nucleotide changes and synonymous (non-coding) nucleotide changes amongst a selection of viral clones, normalized to the proportion of redundant nucleotide residues in the coding sequence. A widely used index is the dN/dS (non-synonymous/synonymous) ratio, defined by Nei and Gojobori19. Such an analysis was applied in the study by Evans et al.18 and revealed clear evidence of positive selection focussed at the CTL epitope-encoding regions in the plasma virion RNA in three macaques. The lack of positive selection for amino acid substitutions in regions of the viral genome containing MHCmismatched CTL epitopes within the same individual, and in corresponding regions of the virus in MHC-mismatched individuals, provided important internal and external controls. Directly comparable results have been previously reported in HIV-1 infection13. The data of Evans et al. also revealed co-evolution of variant sequences on the same RNA strand, providing unequivocal evidence that individual viruses can acquire multiple escape epitopes. This last finding is important, as an evolutionary model of viral escape would predict that single virions should adapt in this way. The work of Evans et al. provides further strong support for the idea that CTLs control immunodeficiency viruses, and that the PII: S0966-842X(00)01706-6
NO. 4
APRIL 2000
COMMENT
selective pressure they exert moulds the viral population during persistent infection. Additionally, this study corroborates earlier work15,16 linking progressive disease with the accumulation of serial escape mutations and thus with loss of CTL control. These data provide a plausible explanation for two observations: the correlation between human leukocyte antigen (HLA) class I homozygosity and accelerated disease progression; and the protective effect of class I heterozygosity20,21. However, uncertainties remain concerning the crucial interactions between HIV and the immune response during the very long period of containment characteristic of chronic viral infection. The simian model does not mimic this part of the disease process precisely, and further human studies are therefore required to address these issues in detail. References 1 Plata, F. et al. (1987) AIDS virus-specific cytotoxic T lymphocytes in lung disorders. Nature 328, 348–351 2 Walker, B.D. et al. (1987) HIV-specific cytotoxic T lymphocytes in seropositive individuals. Nature 328, 345–348 3 Goulder, P. et al. (1997) Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses. Immunol. Rev. 159, 17–29
4 Jin, X. et al. (1999) Dramatic rise in plasma viremia after CD81 T cell depletion in simian immunodeficiency virus-infected macaques. J. Exp. Med. 189, 991–998 5 Schmitz, J.E. et al. (1999) Control of viremia in simian immunodeficiency virus infection by CD81 lymphocytes. Science 283, 857–860 6 Ogg, G.S. et al. (1998) Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA. Science 279, 2103–2106 7 Roberts, J.D. et al. (1988) The accuracy of reverse transcriptase from HIV-1. Science 242, 1171–1173 8 Goodenow, M. et al. (1989) HIV-1 isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions. J. Acquired Immune Defic. Syndr. 2, 344–352 9 Wolinsky, S.M. et al. (1996) Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 272, 537–542 10 Harrigan, P.R. and Alexander, C.S. (1999) Selection of drug-resistant HIV. Trends Microbiol. 7, 120–123 11 Harrigan, P.R. and Alexander, C.S. (1999) Selection of drug-resistant HIV: Erratum. Trends Microbiol. 7, 302 12 Phillips, R.E. et al. (1991) Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition. Nature 354, 453–459 13 Price, D.A. et al. (1997) Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc. Natl. Acad. Sci. U. S. A. 94, 1890–1895 14 Borrow, P. et al. (1997) Antiviral pressure exerted by HIV-1-specific
15
16
17
18
19
20
21
cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat. Med. 3, 205–211 Goulder, P.J. et al. (1997) Late escape from an immunodominant cytotoxic Tlymphocyte response associated with progression to AIDS. Nat. Med. 3, 212–217 Koenig, S. et al. (1995) Transfer of HIV1-specific cytotoxic T lymphocytes to an AIDS patient leads to selection for mutant HIV variants and subsequent disease progression. Nat. Med. 1, 330–336 Brander, C. et al. (1998) Lack of strong immune selection pressure by the immunodominant, HLA- A*0201restricted cytotoxic T lymphocyte response in chronic human immunodeficiency virus-1 infection. J. Clin. Invest. 101, 2559–2566 Evans, D.T. et al. (1999) Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef. Nat. Med. 5, 1270–1276 Nei, M. and Gojobori, T. (1986) Simple methods for estimating the numbers of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426 Tang, J. et al. (1999) HLA class I homozygosity accelerates disease progression in human immunodeficiency virus type 1 infection. AIDS Res. Hum. Retroviruses 15, 317–324 Carrington, M. et al. (1999) HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 283, 1748–1752
Sortase: the surface protein anchoring transpeptidase and the LPXTG motif Richard P. Novick
N
ot so very long ago, staphylococci were considered to be ‘bald’ as they are non-motile and lack macroscopic surface appendages such as the pili or fimbriae found on many bacilli. Although surface appendages remain inapparent, electron microscopy has revealed that, rather than being bald, the organism is a fuzzy ball, being decorated with a myriad of filamentous
proteins that cover essentially the entire visible surface area and, moreover, are rather stably
R.P. Novick is in the Program in Molecular Pathogenesis, Skirball Institute, Depts of Microbiology and Medicine, New York University Medical School, New York, NY 10016, USA. tel: 11 212 263 6290, fax: 11 212 263 8951, e-mail: [email protected]
0966-842X/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved. TRENDS
IN
MICROBIOLOGY
148
VOL. 8
attached. Surface proteins, also found on most other Gram-positive bacteria, have major roles in the interactions of the microorganism with its environment and particularly with the animal host, where they serve as agglutinins and adhesins, block phagocytosis and prevent opsonization. The mechanisms of their export and attachment are therefore of considerable significance for the overall PII: S0966-842X(00)01741-8
NO. 4
APRIL 2000