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Genome Research
Vol. 7, No. 10, pp. 967-973, October 1997
REVIEW
The Role of Genomics in Studying Genetic Susceptibility to Infectious Disease
David Weatherall,1 John Clegg, and Dominic Kwiatkowski
Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
The notion that selection during epidemics or longer periods of exposure to infectious diseases may have had a major effect in modifying the constitution of the human genome is not new. It was proposed, at least in outline, by A.E. Garrod in 1931. In his remarkable book, The Inborn Factors in Disease, he suggested that infectious diseases may have been a major selective force in human evolution and in shaping our biochemical individuality. In 1948, J.B.S. Haldane, unimpressed with the idea that the extremely high frequency of thalassemia in certain racial groups from the Mediterranean region might reflect an unusually high mutation rate in these populations, proposed that these diseases might have come under intense selection because of heterozygote advantage against malaria. It was, in effect, Haldane's remarkable insight that opened up the field of the investigation of genetic susceptibility to infection.
Although considerable progress was made in relating the frequency and distribution of different protein polymorphisms to past or present infection, until recently the field was bedeviled by difficulties relating to population homogeneity, founder effects, and gene drift. However, with an increasing ability to analyze human variability at the DNA level, progress has been much more rapid. Comparing the sequences of genes common to rodents and humans, Murphy (1993), found that host defense genes are much more diverse than those for other families of proteins, an observation suggesting that selection in many species has resulted from exposure to different infectious agents. The way in which DNA analysis is transforming our understanding of the reasons for the distribution and high frequency of the human hemoglobin variants, the problem first posed by Haldane, is reviewed by Flint et al. (1993). Clearly, an analysis of the human genome with respect to variable susceptibility to infection is already beginning to provide important new insights into the mechanisms of human diversity.
In considering genetic susceptibility to infectious disease it is important not only to consider the genetic makeup of the host but also that of the infectious agent. Here, we focus mainly on recent studies of the genetic factors that may modify susceptibility to infection in humans and touch only briefly on some recent developments in microbial genetics that may play an important role in this interaction. Mouse models for studying genetic susceptibility to infection have been reviewed recently elsewhere (McLeod et al. 1995).
Viral Disease
The molecular basis for individual susceptibility to viral disease is becoming clearer, at least in a few diseases. Between 5% and 20% of individuals infected by the hepatitis B virus develop a chronic carrier state that may be associated with liver disease and hepatocellular carcinoma. It has been found recently that different HLA-DR polymorphisms are associated with either chronic carriage or rates of viral clearance (Almari and Batchelor 1994; Thursz et al. 1995).
Another puzzling observation about the natural history of viral illness, that is, why some patients who are regularly exposed to the human immunodeficiency virus (HIV) do not become infected, recently has been explained, at least in part, at the molecular level. Liu et al. (1996) observed that the CD4+ T cells of two such individuals were highly resistant in vitro to the entry of primary macrophage-tropic virus but were readily infected with transformed T-cell-line-adapted viruses. It was found that these individuals were homozygous for a defect in the CKR-5 gene, which codes for the coreceptor for primary HIV-1 isolates. It turned out that they had inherited a defective CRK-5 allele containing an internal 32-bp deletion. The resulting protein is truncated and cannot be detected at the cell surface. This mutation has been observed in other patients who were resistant to HIV infection, although not in all.
Further possible examples of polymorphisms that may modify the response to virus infection are summarized by Hill (1996)
Genome Research
Vol. 7, No. 10, pp. 967-973, October 1997
REVIEW
The Role of Genomics in Studying Genetic Susceptibility to Infectious Disease
David Weatherall,1 John Clegg, and Dominic Kwiatkowski
Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
The notion that selection during epidemics or longer periods of exposure to infectious diseases may have had a major effect in modifying the constitution of the human genome is not new. It was proposed, at least in outline, by A.E. Garrod in 1931. In his remarkable book, The Inborn Factors in Disease, he suggested that infectious diseases may have been a major selective force in human evolution and in shaping our biochemical individuality. In 1948, J.B.S. Haldane, unimpressed with the idea that the extremely high frequency of thalassemia in certain racial groups from the Mediterranean region might reflect an unusually high mutation rate in these populations, proposed that these diseases might have come under intense selection because of heterozygote advantage against malaria. It was, in effect, Haldane's remarkable insight that opened up the field of the investigation of genetic susceptibility to infection.
Although considerable progress was made in relating the frequency and distribution of different protein polymorphisms to past or present infection, until recently the field was bedeviled by difficulties relating to population homogeneity, founder effects, and gene drift. However, with an increasing ability to analyze human variability at the DNA level, progress has been much more rapid. Comparing the sequences of genes common to rodents and humans, Murphy (1993), found that host defense genes are much more diverse than those for other families of proteins, an observation suggesting that selection in many species has resulted from exposure to different infectious agents. The way in which DNA analysis is transforming our understanding of the reasons for the distribution and high frequency of the human hemoglobin variants, the problem first posed by Haldane, is reviewed by Flint et al. (1993). Clearly, an analysis of the human genome with respect to variable susceptibility to infection is already beginning to provide important new insights into the mechanisms of human diversity.
In considering genetic susceptibility to infectious disease it is important not only to consider the genetic makeup of the host but also that of the infectious agent. Here, we focus mainly on recent studies of the genetic factors that may modify susceptibility to infection in humans and touch only briefly on some recent developments in microbial genetics that may play an important role in this interaction. Mouse models for studying genetic susceptibility to infection have been reviewed recently elsewhere (McLeod et al. 1995).
Viral Disease
The molecular basis for individual susceptibility to viral disease is becoming clearer, at least in a few diseases. Between 5% and 20% of individuals infected by the hepatitis B virus develop a chronic carrier state that may be associated with liver disease and hepatocellular carcinoma. It has been found recently that different HLA-DR polymorphisms are associated with either chronic carriage or rates of viral clearance (Almari and Batchelor 1994; Thursz et al. 1995).
Another puzzling observation about the natural history of viral illness, that is, why some patients who are regularly exposed to the human immunodeficiency virus (HIV) do not become infected, recently has been explained, at least in part, at the molecular level. Liu et al. (1996) observed that the CD4+ T cells of two such individuals were highly resistant in vitro to the entry of primary macrophage-tropic virus but were readily infected with transformed T-cell-line-adapted viruses. It was found that these individuals were homozygous for a defect in the CKR-5 gene, which codes for the coreceptor for primary HIV-1 isolates. It turned out that they had inherited a defective CRK-5 allele containing an internal 32-bp deletion. The resulting protein is truncated and cannot be detected at the cell surface. This mutation has been observed in other patients who were resistant to HIV infection, although not in all.
Further possible examples of polymorphisms that may modify the response to virus infection are summarized by Hill (1996)