env gene sequences of primary HIV type 1 isolates of subtypes B, C, D, E, and F obtained from the World Health Organization Network for HIV Isolation and Characterization

Duck plague virus UL41 protein inhibits RIG-I/MDA5-mediated duck IFN-β production via mRNA degradation activity

Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are cytosolic pattern recognition receptors that initiate innate antiviral immunity. Recent reports found that duck RLRs significantly restrict duck plague virus (DPV) infection. However, the molecular mechanism by which DPV evades immune responses is unknown. In this study, we first found that the DPV UL41 protein inhibited duck interferon-β (IFN-β) production mediated by RIG-I and melanoma differentiation-associated gene 5 (MDA5) by broadly downregulating the mRNA levels of important adaptor molecules, such as RIG-I, MDA5, mitochondrial antiviral signalling protein (MAVS), stimulator of interferon gene (STING), TANK-binding kinase 1 (TBK1), and interferon regulatory factor (IRF) 7. The conserved sites of the UL41 protein, E229, D231, and D232, were responsible for this activity. Furthermore, the DPV CHv-BAC-ΔUL41 mutant virus induced more duck IFN-β and IFN-stimulated genes (Mx, OASL) production in duck embryo fibroblasts (DEFs) than DPV CHv-BAC parent virus. Our findings provide insights into the molecular mechanism underlying DPV immune evasion.

[Prevalence of HIV-1 subtypes in patients of an urban center in Southern Brazil]

OBJECTIVE

To estimate the prevalence of HIV-1 subtypes and analyze factors associated.

METHODS

A cross-sectional study was performed with a convenience sample of 80 adult HIV-positive patients, users of an AIDS/STD specialized service, in the city of Canoas, Southern Brazil, between July 2008 and January 2009. Determination of HIV subtypes was performed with the amplification of viral genome fragment, using polymerase chain reaction, followed by sequencing of the amplified fragments. Sociodemographic, clinical and behavioral variables were collected in a structured questionnaire. Univariate statistical analysis was performed, using chi-square test and Student's t-test.

RESULTS

A higher prevalence of subtype C was found (43.8%; 95% CI: 32.9;54.6), followed by CRF31_BC (35.0%; 95% CI: 24.6;45.5) and subtypes B (18.8%; 95% CI: 10.2;27.3) and F (2.4%; 95% CI: 0;5.9). Other HIV-1 subtypes were not observed. Patients infected with CRF31_BC were diagnosed more recently than patients infected with subtype B (p<0.05). In addition, there was a higher frequency of co-infection with other viruses (hepatitis B and C and human T-lymphotropic viruses) in individuals with CRF31_BC, compared to other subtypes. With regard to sociodemographic aspects, there were no differences in the distribution of subtypes and recombinant forms, in terms of gender and sexual practices.

CONCLUSIONS

Results obtained indicate a higher frequency of subtype C and CRF31_BC in this urban center of Southern Brazil, with possible different ways of transmission.

Origin and evolutionary history of HIV-1 subtype C in Brazil

OBJECTIVE

To investigate the origin and to reconstruct the onset date of the HIV-1 subtype C epidemic in Brazil.

DESIGN

Three independent datasets of subtype C sequences isolated from HIV-1-positive patients from southern Brazil over a period of 15 years (1991-2006) were analyzed: 82 env V3 sequences (213 nt), 40 env C2-C5 sequences (559 nt), and 72 pol sequences (960 nt).

METHODS

Brazilian sequences were compared with other subtype C reference strains from the database using basic local alignment search tool, phylogenetic analyses, and searching of specific amino acid signature patterns. Evolutionary parameters were estimated using a Bayesian coalescent-based method under either strict or relaxed molecular clock models.

RESULTS

HIV-1 subtype C sequences from Brazil and Burundi formed a monophyletic cluster at both env and pol regions and shared specific amino acid signatures in the protease region when compared with other viruses of the same subtype from around the world. All Brazilian strains arose as a monophyletic subcluster within the Burundi-Brazilian lineage, whereas isolates from Burundi appeared at the origin of the clade. Evolutionary analyses of both env and pol genomic regions indicate that the age of the most recent common ancestor of the Brazilian subtype C clade dates back to the early 1980s.

CONCLUSION

The subtype C epidemic in the southern Brazilian region was initiated by the introduction of a single founder strain closely related to subtype C strains from Burundi. Our results suggest that this founder event probably took place around the early 1980s, roughly a decade before the previous estimates.

On the origin of HIV-1 subtype C in South America

OBJECTIVE

Our aim was to investigate the monophyletic status of the HIV-1C that circulates in South America and its phylogenetic relationships with other HIV-1C populations around the world in order to shed light on its the geographic origins as well as the place of introduction in the continent.

METHODS

Fifty-one sequences from South America and 46 from non-South American countries, including samples from Africa and Asia, were obtained from the Los Alamos National Laboratory. The data analyzed corresponded to the entire protease and two-thirds of the polymerase domain from the reverse transcriptase. Phylogenetic analyses using maximum likelihood and Bayesian inference were performed in Phylogenetic Analysis Using Parsymony, PHYlogenetic inferences using Maximum Likelihood, and MrBayes.

RESULTS

Samples from South America formed a monophyletic group independent of the method used. The bootstrap support of South American HIV-1C was higher than 60% in maximum likelihood trees and its posterior probability was 99% in the Bayesian analysis. These results indicate the monophyletic nature of the South American HIV-1C. Moreover, in all trees estimated, a sequence from Kenya was the most closely related to the South American clade, followed by two from Ethiopia. All South American sequences from countries other than Brazil showed closer phylogenetic relatedness to Brazilian samples, indicating that HIV-1C was introduced in South America in Brazil.

CONCLUSION

Our results indicate that the entry of HIV-1C in South America occurred in a single episode or in multiples episodes of genetically related viruses, possibly from an eastern African country. HIV-1C was then disseminated to the remaining South American countries from Brazil.

Functional chimeras of human immunodeficiency virus type 1 Gp120 and influenza A virus (H3) hemagglutinin

In an attempt to produce a protein that will allow determination of the native human immunodeficiency virus type 1 (HIV-1) gp120 (Env) structure in its trimeric state, we fused the globular head of gp120 to the stalk region of influenza virus A (X31) hemagglutinin (HA). The chimeric protein (EnvHA) has been expressed by using a recombinant vaccinia virus system, and its functional characteristics were determined. EnvHA is expressed as a 120- to 150-kDa protein that can oligomerize to form dimers and trimers. It retains the low-pH (5.2 to 5.4) requirement of X31-HA to trigger membrane fusion but, unlike X31-HA, it is not absolutely dependent on exogenously added trypsin for protein processing to release the HA2 fusion peptide. In terms of receptor binding the chimeric protein retains specificity for human CD4 but, in relation to the membrane fusion event, it appears to lose the Env coreceptor specificity of the parental HIV-1 strains: NL43 for CXCR4 and JRFL for CCR5. These properties suggest that stable, functional EnvHAs are being produced and that they may be exploited in terms of structural studies. Further, the potential of introducing the envHA genes into influenza viruses, by use of reverse genetics, and their use as a therapeutic vaccine for HIV are discussed.

An unrelated monoclonal antibody neutralizes human immunodeficiency virus type 1 by binding to an artificial epitope engineered in a functionally neutral region of the viral envelope glycoproteins

Neutralizing antibodies often recognize regions of viral envelope glycoproteins that play a role in receptor binding or other aspects of virus entry. To address whether this is a necessary feature of a neutralizing antibody, we identified the V4 region of the gp120 envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) as a sequence that is tolerant of drastic change and thus appears to play a negligible role in envelope glycoprotein function. An artificial epitope tag was inserted into the V4 region without a significant effect on virus entry or neutralization by antibodies that recognize HIV-1 envelope glycoprotein sequences. An antibody directed against the artificial epitope tag was able to neutralize the modified, but not the wild-type, HIV-1. Thus, the specific target of a neutralizing antibody need not contribute functionally to the process of virus entry.

Analysis of full-length HIV type 1 env genes indicates differences between the virus infecting T cells and dendritic cells in peripheral blood of infected patients

Dendritic cells (DC) are targets for HIV-1 infection and may harbor distinct populations of virus variants. To test this hypothesis full length env genes have been amplified and sequenced from DC and T cells purified from the blood of five symptomatic HIV-1-infected patients. For three of the patients, showing slow and slow/standard disease progression, distinct subsets of HIV variants infected DC and T cells, and the diversity of the DC-derived env genes was less than that observed in T cells. Amino acid substitutions differentiating DC and T cell variants were dispersed throughout the length of the glycoproteins and were patient/HIV-1 strain specific. However, the V1 and V2 domains of T cell-derived clones were generally shorter than those from DC. These findings suggest that there may be distinct populations of HIV-1 variants infecting blood DC and T cells in patients showing slow and slow/standard disease progression.

An HIV type 1 subtype B founder effect in Korea: gp160 signature patterns infer circulation of CTL-escape strains at the population level

HIV-1 subtype B predominates in the Republic of Korea. Phylogenetic analyses of sequences for complete nef genes and env gene fragments encoding the V3 loop have identified a major monophyletic Korean subclade that is distinct from Western subtype B sequences in the Los Alamos HIV Sequence Database. This was investigated further by sequence analysis of complete env genes recovered from the DNA of peripheral blood mononuclear cells for matched groups of Koreans, four patients per group, previously assigned as being infected with either Korean or Western strains. The phylogenetic classifications were confirmed and analysis of the translation products identified 32 amino acid signature pattern differences, dispersed throughout gp160, which differentiate the two subclades. Twenty-three of these positions map to epitopes recognized by HLA-I-restricted cytotoxic T-lymphocytes (CTL) as catalogued in the Los Alamos HIV Immunology Database. The remaining nine map at or close to sites predicted to be targets for immunoproteasomes that are involved in producing peptides that bind to MHC Class I. These results suggest that a founder effect in the Korean population is based on the spread of CTL-escape/host-adapted HIV-1 strains.

Early evolution of the human immunodeficiency virus type 1 subtype C epidemic in rural Malawi

We have tracked the early years of the evolution of the human immunodeficiency virus type 1 (HIV-1) epidemic in a rural district of central east Africa from the first documented introductions of subtypes A, D, and C to the present predominance of subtype C. The earliest subtype C sequences ever reported are described. Blood samples were collected on filter papers from 1981 to 1984 and from 1987 to 1989 from more than 44,000 individuals living in two areas of Karonga District, Malawi. These samples included HIV-1-positive samples from 200 people. In 1982 to 1984, HIV-1 subtypes A, C, and D were all present, though in small numbers. By 1987 to 1989, 152 (90%) of a total of 168 sequences were subtype C and AC, AD, and DC recombinants had emerged. Four of the subtype C sequences from 1983 to 1984 were closely related and were found at the base of a large cluster of low diversity that by the late 1980s accounted for 40% of C sequences. The other two early C sequences fell into a separate and more diverse cluster. Three other clusters containing sequences from the late 1980s were identified. Each cluster contained at least one sample from a person who had recently arrived in the district. From 18 HIV-1-positive spouse pairs, 12 very closely related pairs of sequences were identified. We conclude that there were multiple introductions of HIV-1 with limited spread, followed by explosive growth of a subtype C cluster, probably arising from a single introduction in or before 1983.

Tenofovir, adefovir, and zidovudine susceptibilities of primary human immunodeficiency virus type 1 isolates with non-B subtypes or nucleoside resistance

New antiretroviral drugs with activity against strains of human immunodeficiency virus type 1 (HIV-1) with non-B subtypes and with resistance to current antiretroviral drugs are needed. The activity of two nucleotide analogs, tenofovir and adefovir (PMPA and PMEA, respectively), against non-B subtypes and nucleoside-resistant primary HIV-1 isolates was assessed. Tenofovir and adefovir were fully active against a panel of subtypes A, C, D, E, F, G, and group O primary HIV-1 isolates as compared with their respective activity against subtype B isolates. Moreover, the susceptibility of a panel of 10 primary HIV-1 isolates with >10-fold mean resistance to zidovudine, lamivudine, and abacavir was within 2.2-fold of wild-type tenofovir susceptibility for each isolate. An oral prodrug of tenofovir, tenofovir disoproxil fumarate (DF), is currently in phase III clinical trials for the treatment of HIV-1 infection. These in vitro susceptibility results suggest that tenofovir DF may be active in vivo against HIV-1 with nucleoside resistance as well as against HIV-1 with non-B subtypes.

Near full-length clones and reference sequences for subtype C isolates of HIV type 1 from three different continents

Among the major circulating HIV-1 subtypes, subtype C is the most prevalent. To generate full-length subtype C clones and sequences, we selected 13 primary (PBMC-derived) isolates from Zambia, India, Tanzania, South Africa, Brazil, and China, which were identified as subtype C by partial sequence analysis. Near full-length viral genomes were amplified by using a long PCR technique, sequenced in their entirety, and phylogenetically analyzed. Amino acid sequence analysis revealed 10.2, 6.3, and 17.3% diversity in predicted Gag, Pol, and Env protein sequences. Ten of 13 viruses were nonmosaic subtype C genomes, while all three isolates from China represented B/C recombinants. One of them was composed primarily of subtype C sequences with three small subtype B portions in gag, pol, and nef genes. Two others exhibited these same mosaic regions, but contained two additional subtype B portions at the gag/pol overlap and in the accessory gene region, suggesting ongoing B/C recombination in China. All subtype C genomes contained a prematurely truncated second exon of rev, but other previously proposed subtype C signatures, including three potential NF-kappa B-binding sites in the viral promoter-enhancer regions, were found in only a subset of these genomes.

The explosive human immunodeficiency virus type 1 epidemic among injecting drug users of Kathmandu, Nepal, is caused by a subtype C virus of restricted genetic diversity

An explosive epidemic of human immunodeficiency virus type 1 (HIV-1) has been documented among the injecting drug user population of Kathmandu, Nepal, whose seropositivity rate has risen from 0 to 40% between 1995 and 1997. By using Catrimox to preserve whole-blood RNA at ambient temperature for transportation, HIV-1 envelope V3-V4 sequences were obtained from 36 patients in this group. Analysis of the sequences indicated a homogenous epidemic of subtype C virus, with at least two independent introductions of the virus into the population. Viral diversity was restricted within two transmission subclusters, with the majority of variation occurring in V4. Calculation of the synonymous-to-nonsynonymous mutation ratio (Ks:Ka) across this region showed that significant evolutionary pressure had been experienced during the rapid horizontal spread of the virus in this population, most strongly directed to the region between V3 and V4.

Sequence variations in human immunodeficiency virus type 1 Nef are associated with different stages of disease

nef alleles derived from a large number of individuals infected with human immunodeficiency virus type 1 (HIV-1) were analyzed to investigate the frequency of disrupted nef genes and to elucidate whether specific amino acid substitutions in Nef are associated with different stages of disease. We confirm that deletions or gross abnormalities in nef are rarely present. However, a comparison of Nef consensus sequences derived from 41 long-term nonprogressors and from 50 individuals with progressive HIV-1 infection revealed that specific variations are associated with different stages of infection. Five amino acid variations in Nef (T15, N51, H102, L170, and E182) were more frequently observed among nonprogressors, while nine features (an additional N-terminal PxxP motif, A15, R39, T51, T157, C163, N169, Q170, and M182) were more frequently found in progressors. Strong correlations between the frequency of these variations in Nef and both the CD4(+)-cell count and the viral load were observed. Moreover, analysis of sequential samples obtained from two progressors revealed that several variations in Nef, which were more commonly observed in patients with low CD4(+)-T-cell counts, were detected only during or after progression to immunodeficiency. Our results indicate that sequence variations in Nef are associated with different stages of HIV-1 infection and suggest a link between nef gene function and the immune status of the infected individual.

Enhanced replication of M-tropic HIV-1 strains in Herpesvirus saimiri immortalised T-cells which express CCR5

A better characterisation of mononuclear cell-tropic (M-tropic) HIV-1 is central to disease control as these viruses predominate in disease transmission. M-tropic viruses do not replicate in conventional T-cell lines, and virus titres obtained in peripheral blood mononuclear cells (PBMC) are low. Human T-lymphocytes which have been immortalised by Herpesvirus saimiri strain C488 (HVS T-cells) are highly permissive to the replication of T-cell tropic strains of HIV. This study aimed to determine if HVS T-cells support replication of M-tropic HIV isolates that have not been adapted to conventional T-cell lines. A panel of PBMC low passage/primary field isolates and their molecular clones was used. Results show that infection in HVS T-cells was longer lived than in PBMC. In terms of peak virus titre and duration of productive infection, the two HVS T-cell lines studied were superior to PBMC, and one supported enhanced replication of all M-tropic isolates. This is important for generating M-tropic virus pools of sufficient titre for further biological studies such as virus neutralisation, co receptor usage and testing of antivirals. Phenotypic analysis showed that HVS T-cells are CD4+-activated memory cells expressing both CXCR-4 and CCR5 co receptors. Thus, HVS immortalisation appears to select for the T-cell subset targeted by HIV-1 in vivo.

Association between a defective CCR-5 gene and progression to disease in HIV infection

We measured the effect(s) of CCR-5 genotype on disease progression by studying the frequency of a defective CCR-5 delta32 allele within a cohort of long-term infected individuals. An elevated frequency of CCR-5 delta32 heterozygotes within the cohort compared with a control population of blood donors was observed. An association between progression rate and CCR-5 delta32 heterozygosity was observed. Furthermore, analysis of proviral DNA V3 sequences from a subset of the cohort predicted that the majority of individuals (39 of 44) were infected with viruses predicted to utilize the beta-chemokine receptor CCR-5. The marked association between CCR-5 genotype and disease progression observed in this study may be a consequence of the predicted low frequency of CXCR-4-utilizing viruses present within the selected cohort.

RNA virus mutations and fitness for survival

RNA viruses exploit all known mechanisms of genetic variation to ensure their survival. Distinctive features of RNA virus replication include high mutation rates, high yields, and short replication times. As a consequence, RNA viruses replicate as complex and dynamic mutant swarms, called viral quasispecies. Mutation rates at defined genomic sites are affected by the nucleotide sequence context on the template molecule as well as by environmental factors. In vitro hypermutation reactions offer a means to explore the functional sequence space of nucleic acids and proteins. The evolution of a viral quasispecies is extremely dependent on the population size of the virus that is involved in the infections. Repeated bottleneck events lead to average fitness losses, with viruses that harbor unusual, deleterious mutations. In contrast, large population passages result in rapid fitness gains, much larger than those so far scored for cellular organisms. Fitness gains in one environment often lead to fitness losses in an alternative environment. An important challenge in RNA virus evolution research is the assignment of phenotypic traits to specific mutations. Different constellations of mutations may be associated with a similar biological behavior. In addition, recent evidence suggests the existence of critical thresholds for the expression of phenotypic traits. Epidemiological as well as functional and structural studies suggest that RNA viruses can tolerate restricted types and numbers of mutations during any specific time point during their evolution. Viruses occupy only a tiny portion of their potential sequence space. Such limited tolerance to mutations may open new avenues for combating viral infections.

HIV/SIV glycoproteins: structure-function relationships

The various functions of human (HIV) and simian (SIV) immunodeficiency virus glycoproteins are similar, so it may be assumed that the overall structure of the folded proteins will be maintained. To preserve structure there must be constraints on sequence variation. The majority of mutations tolerated will be involved in immune escape but changes at some positions are known to have direct effects on glycoprotein expression and function. This allows the virus to change its phenotype and escape immune pressure. These properties will influence the fitness of the virus to infect and replicate in potential hosts. A better understanding of the structure-function relationships of HIV/SIV glycoproteins will assist in the development of vaccines and antivirals. Here, we identify similarities and differences between HIV-1 subtypes and HIV/SIV types that may be relevant to the phenotypes of the various groups. The results are discussed in relation to what is known of domain-function associations for HIV/SIV glycoproteins.