Host genetics and viral infections: immunology taught by viruses, virology taught by the immune system

Ascarid infection in wild Amur tigers (Panthera tigris altaica) in China

BACKGROUND

Wild Amur tigers are a sparsely populated species, and the conservation of this species is of great concern worldwide, but as an important health risk factor, parasite infection in them is not fully understanding.

RESULTS

In this study, sixty-two faecal samples were collected to investigate the frequency and infection intensity of Toxocara cati and Toxascaris leonina in wild Amur tigers. The T. cati and T. leonina eggs were preliminary identified by microscopy, and confirmed by molecular techniques. Infection intensity was determined by the modified McMaster technique. Phylogenetic trees demonstrated that T. cati of wild Amur tiger had a closer relationship with which of other wild felines than that of domestic cats. T. leonina of Amur tiger and other felines clustered into one clade, showing a closer relationship than canines. The average frequency of T. cati was 77.42% (48/62), and the frequency in 2016 (100%) were higher than those in 2013 (P = 0.051, < 0.1; 66.6%) and 2014 (P = 0.079, < 0.1; 72.2%). The infection intensity of T. cati ranged from 316.6 n/g to 1084.1 n/g. For T. leonina, only three samples presented eggs when the saturated sodium chloride floating method was performed, indicating that the frequency is 4.83% (3/62). Unfortunately, the egg number in faecal smears is lower than the detective limitation, so the infection intensity of T. leonina is missed.

CONCLUSIONS

This study demonstrated that ascarids are broadly prevalent, and T. cati is a dominant parasite species in the wild Amur tiger population.

Mutualistic viruses and the heteronomy of life

Though viruses have generally been characterized by their pathogenic and more generally harmful effects, many examples of mutualistic viruses exist. Here I explain how the idea of mutualistic viruses has been defended in recent virology, and I explore four important conceptual and practical consequences of this idea. I ask to what extent this research modifies the way scientists might search for new viruses, our notion of how the host immune system interacts with microbes, the development of new therapeutic approaches, and, finally, the role played by the criterion of autonomy in our understanding of living things. Overall, I suggest that the recognition of mutualistic viruses plays a major role in a wider ongoing revision of our conception of viruses.

HIV-1 control in battlegrounds: important host genetic variations for HIV-1 mother-to-child transmission and progression to clinical pediatric AIDS

HIV-1 mother-to-child transmission (MTCT) is the passing of maternal HIV-1 to the offspring during pregnancy, labor and delivery, and/or breastfeeding. HIV-1 MTCT and the evolution to pediatric AIDS are multifactorial, dynamic and variable phenotypic conditions. Both genetic and nongenetic variables can influence susceptibility to HIV-1 MTCT or the rate of progression to clinical pediatric AIDS. In this review, we summarize the current state of knowledge about the roles of genetic variations seen in host immune response genes, and those that have been independently associated, mostly through population genetics of candidate genes, with interindividual susceptibility to HIV-1 MTCT, and progression to pediatric AIDS. We examine common and rare host genetic variations at coding and noncoding polymorphisms, whether functional or not, in agonists and antagonists of the immune response, which have been implicated in HIV-1 control in battlegrounds of cell entry, replication and evolution to AIDS. Further, we point to over 380 single-nucleotide polymorphisms, mostly within the HLA super region, recently identified in unbiased genome-wide association studies of HIV replication and evolution in adults, still unexplored in the context of HIV-1 MTCT, and which are likely to also influence susceptibility to pediatric HIV-1/AIDS.

HLA-B57 and gender influence the occurrence of tuberculosis in HIV infected people of south India

BACKGROUND

Substantial evidence exists for HLA and other host genetic factors being determinants of susceptibility or resistance to infectious diseases. However, very little information is available on the role of host genetic factors in HIV-TB coinfection. Hence, a longitudinal study was undertaken to investigate HLA associations in a cohort of HIV seropositive individuals with and without TB in Bangalore, South India.

METHODS

A cohort of 238 HIV seropositive subjects were typed for HLA-A, B, and DR by PCR-SSP and followed up for 5 years or till manifestation of Tuberculosis. HLA data of 682 HIV Negative healthy renal donors was used as control.

RESULTS

The ratio of males and females in HIV cohort was comparable (50.4% and 49.6%). But the incidence of TB was markedly lower in females (12.6%,) than males (25.6%). Further, HLA-B*57 frequency in HIV cohort was significantly higher among females without TB (21.6%, 19/88) than males (1.7%, 1/59); P = 0.0046; OR = 38. CD4 counts also were higher among females in this cohort.

CONCLUSION

This study suggests that HIV positive women with HLA-B*57 have less occurrence of TB as compared to males.

Eca20 microsatellite polymorphisms in equine viral arteritis-infected horses from Argentina

We investigated the association of equine arteritis virus (EAV) infection and three short tandem repeat (STR) polymorphisms located within or in close proximity to equine lymphocyte antigen (ELA) region. We used a case-control design as a first approach before proceeding to select candidate genes. One hundred and sixty-five Silla Argentino horses were taken in 2002 from positive serological detections of EAV in Argentina, to determine whether STR genotypes were correlated to genetic susceptibility to EVA. Allele frequency distribution did not show significant differences between both groups (P = 0.0781). However, in particular alleles, Fisher exact test and odds ratio calculations showed significant values >1 for TKY08 and LEX52, and <1 for UM011, TKY08, LEX52 and VHL20. Interestingly, TKY08 STR is located in ELA class I region.

Emergence of variability in isogenic Escherichia coli populations infected by a filamentous virus

The spread of epidemics not only depends on the average number of parasites produced per host, but also on the existence of highly infectious individuals. It is widely accepted that infectiousness depends on genetic and environmental determinants. However, even in clonal populations of host and viruses growing in homogeneous conditions, high variability can exist. Here we show that Escherichia coli cells commonly display high differentials in viral burst size, and address the kinetics of emergence of such variability with the non-lytic filamentous virus M13. By single-cell imaging of a virally-encoded fluorescent reporter, we monitor the viral charge distribution in infected bacterial populations at different time following infection. A mathematical model assuming autocatalytic virus replication and inheritance of bacterial growth rates quantitatively reproduces the experimental distributions, demonstrating that deterministic amplification of small host inhomogeneities is a mechanism sufficient to explain large and highly skewed distributions. This mechanism of amplification is general and may occur whenever a parasite has an initial phase of exponential growth within its host. Moreover, it naturally reproduces the shift towards higher virulence when the host is experimenting poor conditions, as observed commonly in host-parasite systems.

Adaptive interactions between HLA and HIV-1: highly divergent selection imposed by HLA class I molecules with common supertype motifs

Currently, 1.1 million individuals in the United States are living with HIV-1 infection. Although this is a relatively small proportion of the global pandemic, the remarkable mix of ancestries in the United States, drawn together over the past two centuries of continuous population migrations, provides an important and unique perspective on adaptive interactions between HIV-1 and human genetic diversity. HIV-1 is a rapidly adaptable organism and mutates within or near immune epitopes that are determined by the HLA class I genotype of the infected host. We characterized HLA-associated polymorphisms across the full HIV-1 proteome in a large, ethnically diverse national United States cohort of HIV-1-infected individuals. We found a striking divergence in the immunoselection patterns associated with HLA variants that have very similar or identical peptide-binding specificities but are differentially distributed among racial/ethnic groups. Although their similarity in peptide binding functionally clusters these HLA variants into supertypes, their differences at sites within the peptide-binding groove contribute to race-specific selection effects on circulating HIV-1 viruses. This suggests that the interactions between the HLA/HIV peptide complex and the TCR vary significantly within HLA supertype groups, which, in turn, influences HIV-1 evolution.

Host factors associated with outcome from primary human immunodeficiency virus-1 infection

PURPOSE OF REVIEW

The early events in human immunodeficiency virus-1 infection are increasingly recognized as critical for the overall evolution of the disease. Viral and host factors interact to establish a point of equilibrium defined by the viral set point. This review highlights new opportunities in the understanding of the genetic and genomic determinants of those early events.

RECENT FINDINGS

The field of human immunodeficiency virus host genetics is shifting from the measure of long-term consequences of infection to the analysis of quantitative biological endpoints of viral control, with particular attention on the earliest events as study phenotypes. The field has also been enriched by a better understanding of the determinant and complex role of human leukocyte antigen and killer cell immunoglobulin-like-receptor variation, and by the completion of the first genome-wide study of determinants of human immunodeficiency virus-1 replication. The genome analysis highlights the central influence of acquired immunity in viral control, and provides an extensive catalogue of novel gene candidates.

SUMMARY

Host genetics and genomic analyses of precise quantitative study phenotypes offer an unprecedented opportunity to dissect critical steps in human immunodeficiency virus-1 pathogenesis.

Comparative and developmental study of the immune system in Xenopus

Xenopus laevis is the model of choice for evolutionary, comparative, and developmental studies of immunity, and invaluable research tools including MHC-defined clones, inbred strains, cell lines, and monoclonal antibodies are available for these studies. Recent efforts to use Silurana (Xenopus) tropicalis for genetic analyses have led to the sequencing of the whole genome. Ongoing genome mapping and mutagenesis studies will provide a new dimension to the study of immunity. Here we review what is known about the immune system of X. laevis integrated with available genomic information from S. tropicalis. This review provides compelling evidence for the high degree of similarity and evolutionary conservation between Xenopus and mammalian immune systems. We propose to build a powerful and innovative comparative biomedical model based on modern genetic technologies that takes take advantage of X. laevis and S. tropicalis, as well as the whole Xenopus genus. Developmental Dynamics 238:1249-1270, 2009. (c) 2009 Wiley-Liss, Inc.

The pathogenesis of liver disease in the setting of HIV–hepatitis B virus coinfection

There are many potential reasons for increased liver-related mortality in HIV–hepatitis B virus (HBV) coinfection compared with either infection alone. HIV infects multiple cells in the liver and might potentially alter the life cycle of HBV, although evidence to date is limited. Unique mutations in HBV have been defined in HIV–HBV-coinfected individuals and might directly alter pathogenesis. In addition, an impaired HBV- specific T-cell immune response is likely to be important. The roles of microbial translocation, immune activation and increased hepatic stellate cell activation will be important areas for future study.

FIV cross-species transmission: an evolutionary prospective

Feline and primate immunodeficiency viruses (FIVs, SIVs, and HIV) are transmitted via direct contact (e.g. fighting, sexual contact, and mother–offspring transmission). This dynamic likely poses a behavioral barrier to cross-species transmission in the wild. Recently, several host intracellular anti-viral proteins that contribute to species-specificity of primate lentiviruses have been identified revealing adaptive mechanisms that further limit spread of lentiviruses between species. Consistent with these inter-species transmission barriers, phylogenetic evidence supports the prediction that FIV transmission is an exceedingly rare event between free-ranging cat species, though it has occurred occasionally in captive settings. Recently we documented that puma and bobcats in Southern California share an FIV strain, providing an opportunity to evaluate evolution of both viral strains and host intracellular restriction proteins. These studies are facilitated by the availability of the 2× cat genome sequence annotation. In addition, concurrent viral and host genetic analyses have been used to track patterns of migration of the host species and barriers to transmission of the virus within the African lion. These studies illustrate the utility of FIV as a model to discover the variables necessary for establishment and control of lentiviral infections in new species.

Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection

Outcomes of infection with hepatitis C virus (HCV) vary widely, from asymptomatic clearance to chronic infection, leading to complications that include fibrosis, cirrhosis, hepatocellular carcinoma, and liver failure. Previous studies have reported statistical associations between human leukocyte antigen (HLA) heterozygosity and favorable outcomes of infection with either hepatitis B virus (HBV) or human immunodeficiency virus (HIV) (the "heterozygote advantage"). To investigate whether HLA zygosity is associated with outcome of HCV infection, we used data from the United States Organ Procurement and Transplantation Network database of 52,435 liver transplant recipients from 1995 through 2005. Of these, 30,397 were excluded for lack of HLA data, retransplantation, known HIV infection, or insufficient information regarding HBV infection. The remaining cases were analyzed for associations between HCV infection and HLA zygosity with 1-sided Fisher's exact tests. Results show significantly lower proportions of HLA-DRB1 heterozygosity among HCV-infected than uninfected cases. The differences were more pronounced with alleles represented as functional supertypes (P = 1.05 x 10(-6)) than as low-resolution genotypes (P = 1.99 x 10(-3)). No significant associations between zygosity and HCV infection were found for other HLA loci.

CONCLUSION

These findings constitute evidence for an advantage among carriers of different supertype HLA-DRB1 alleles against HCV infection progression to end-stage liver disease in a large-scale, long-term study population. Considering HLA polymorphism in terms of supertype diversity is recommended in strategies to design association studies for robust results across populations and in trials to improve treatment options for patients with chronic viral infection. Access to deidentified clinical information relating genetic variation to viral infection improves understanding of variation in infection outcomes and might help to personalize medicine with treatment options informed in part by human genetic variation.

Point, Counterpoint: The Evolution of Pathogenic Viruses and their Human Hosts

Viral pathogens play a prominent role in human health owing to their ability to rapidly evolve creative new ways to exploit their hosts. As elegant and deceptive as many viral adaptations are, humans and their ancestors have repeatedly answered their call with equally impressive adaptations. Here we argue that the coevolutionary arms race between humans and their viral pathogens is one of the most important forces in human molecular evolution, past and present. With a focus on HIV-1 and other RNA viruses, we highlight recent developments in our understanding of the human innate and adaptive immune systems and how the selective pressures exerted by viruses have shaped the human genome. We also discuss how the antiviral function of cellular machinery like RNAi and APOBEC3G blur the lines between innate and adaptive immunity. The remarkable power of natural selection is revealed in each host-pathogen arms race examined.