Extremely rapid spread of human immunodeficiency virus type 1 BF recombinants in Argentina

Molecular and geographic characterization of hiv-1 bf recombinant viruses

The Human Immunodeficiency Virus Type 1 (HIV-1) presents a wide genetic variability, which is represented by four groups, nine subtypes of group M and several recombinant forms. Among these, the BF recombinants have been distinguished by a high global dispersion and an increase in number and diversity. To date, 15 BF Circulating Recombinant Forms (CRFs) and diverse BF Unique Recombinant Forms (URFs) have been described. In Brazil, nine CRF_BF have been identified. The aim of this work was to perform molecular and geographic characterization of HIV-1 BF recombinant strains. Near full-length genomes of 265 BF recombinant viruses were collected from public databases and molecular analyses were performed. These sequences were originally retrieved between 1993-2006 and isolated from 16 countries (51.3% from Brazil). Diagnostic's year analysis showed that BF recombinants circulate in Brazil since at least 1985. Most sequences displayed recombination in the pol (84.9%), gag (69.3%) and env (51.4%) regions. The subtype B predominated in all accessory and regulatory genes, except in vif, in which the F subtype was predominant (40.4%). Twelve regions with a recombination rate higher than 10% were identified, especially one region inside p24 gene (1359-1397) whose recombination was present in more than 30% of the sequences. Coreceptor usage prediction during viral entry showed that BF recombinants preferentially use CCR5 (67.2%) and the most frequent tetrapeptides found in the V3 loop were GPGR (47.9%) and GPGQ (21.1%). The frequency of X4/dual viruses was lower amongst F subtype (25.8%) V3 sequences, compared with B subtype (43%). In addition, mutations associated with intermediate or high resistance levels to PI (10.6%), NRTI (15.0%), NNRTI (14.0%) and INSTI (2.6%) were identified. The great diversity of the recombination patterns evidences that the recombination between the subtypes B and F is frequent, reflecting a probable high rate of dual infection and the acquisition of advantageous characteristics for viral fitness.

Genetic Diversity of HIV-1 Gene vif Among Treatment-Naive Brazilians

HIV-1 has the Vif protein, which binds to human antiviral proteins APOBEC3 to form complexes to be degraded by cellular proteolysis. To further explore HIV-1 diversity at the population level, we analyzed blood samples from 317 treatment-naive patients in Brazil. In this study, we explored the correlations of Vif polymorphisms with clinical parameters of the patients and found that mutation K22H is associated with low CD4⁺ cell counts and higher viral loads. Phylogenetic analysis of the vif gene indicated that subtype B was predominant in ∼77% (243/317) of the patients, followed by HIV-1 F ∼18% (56/317), and subtype C ∼4% (12/317); five samples were BF recombinants (∼1% of patients), and one was an AG recombinant. On the basis of the vif gene, we detected the presence of one AG and several previously unknown BF intersubtypes in this population. The global mean diversity, measured by pairwise distances, was 0.0931 ± 0.0006 among sequences of subtype B (n = 243), whereas the mean diversity of subtype C sequences (n = 12) was 0.0493 ± 0.001 and that of subtype F (n = 56) was 0.050 ± 0.001.

Increase in human immunodeficiency virus 1 diversity and detection of various subtypes and recombinants in north-eastern Brazil

PURPOSE

Diverse human immunodeficiency virus 1 (HIV-1) subtypes and circulating recombinant forms are found in Brazil. The majority of HIV-1 molecular epidemiological studies in Brazil have been conducted in the southern and south-eastern regions of the country, although several recent studies in the north-eastern region have addressed this issue. The objective of this study was to molecularly characterize HIV-1 circulating in Pernambuco, north-eastern Brazil.

METHODOLOGY

A total of 64 samples were collected from 2002 to 2003, and another 103 were collected from 2007 to 2009. The protease and partial reverse transcriptase regions of the HIV-1 polymerase-encoding (pol) gene were sequenced, and subtyping, recombination and phylogenetic analyses were performed.Results/Key findings. Subtype B (60.9 %) was found to be predominant, followed by HIV-1 F (31.4 %). Several BF recombinants (4.2 %), and BC and AG recombinants were also identified. The intra-subtype genetic diversity was estimated to be 0.065 (sd±0.004) for HIV-1 B and 0.055 (sd±0.004) for HIV-1 F, reflecting a greater accumulation of mutations in subtype B (P<0.01). More codons were found to be under positive selective pressure in samples collected from 2007 to 2009, from individuals with a T-cell count≥200 cells mm-3 and from women. Coalescence data indicated that the subtype F population has been continuously expanding.

CONCLUSIONS

HIV-1 shows high genetic diversity in the state of Pernambuco. Thus, additional molecular evaluations of circulating strains will provide a better understanding of the epidemic and may lead to more effective preventive strategies.

Time-Dependent Rate Phenomenon in Viruses

Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses.

IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.

Contribution of recombination to the evolutionary history of HIV

PURPOSE OF REVIEW

An improved understanding of how recombination affects the evolutionary history of HIV is crucial to understand its current and future evolution. The present review aims to disentangle the manifold effects of recombination on HIV by discussing its effects on the evolutionary history and the adaptive potential of HIV in the context of concepts from evolutionary genetics and genomics.

RECENT FINDINGS

The increasing occurrence of secondary contacts between divergent subtype populations (during coinfection) results in increased observations of recombinants worldwide. Recombination is heterogeneous along the HIV genome. Consequences of recombination of HIV evolution are, in combination with other demographic processes, expected to either homogenize the genetic composition of HIV populations (homogenization) or provide the potential for novel adaptations (diversification). New methods in population genomics allow deep characterization of recombinant genome (the segment composition and origin) and their evolutionary trajectories.

SUMMARY

HIV recombinants increase worldwide and invade geographical regions where pure subtypes were previously predominant. This trend is expected to continue in the future, as ease to travel worldwide increases opportunities for recombination between divergent HIV strains. While the effects of recombination in HIV are much researched, more effort is required to characterize current HIV recombinant composition and dynamics. This can be achieved with new population genetic and genomic methods.

Near Full-Length Characterization and Population Dynamics of the Human Immunodeficiency Virus Type I Circulating Recombinant Form 42 (CRF42_BF) in Luxembourg

A new recombinant form representing a mosaic of HIV-1 subtype B and F1 and designated as CRF42_BF was identified in Luxembourg. We confirmed the inedited nature of CRF42_BF by near full-length genome characterization and retrieved a possible ancestor originating from Brazil. The demographic history of CRF42_BF in Luxembourg using Bayesian coalescent-based methods was investigated. The exponential phase of the logistic growth happened in a very short time period of approximately 5 months associated with a high mean rate of population growth of 15.02 new infections per year. However, CRF42_BF was not characterized by either a higher ex vivo replication capacity in peripheral blood mononuclear cells (PBMCs) or a higher ex vivo transmission efficiency from monocyte-derived dendritic cells to PBMCs as compared to B and F1 viruses. These data do not support a high pathogenic potential of CFR42_BF but rather an initial bursting spread of the recombinant probably due to a more favorable transmission route.

Endogenous viruses: Connecting recent and ancient viral evolution

The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.

[Sensitivity of the COBAS AmpliScreen™ HIV-1 test v1.5 for HIV-1 detection]

The introduction of nucleic acid amplification techniques (NAT) in blood banks was intended to reduce the residual risk of transfusion-transmitted infections. Co-circulation of a great diversity of HIV-1 variants in Argentina portrays the need to assess the sensitivity of serological and molecular assays available for their detection. In this study, we evaluated the sensitivity of the COBAS AmpliScreen™ HIV-1 Test, version 1.5 (Roche) for the detection of HIV-1 RNA in plasma samples of infected individuals from Argentina. The results of this study reveal that this technique has high sensitivity for the detection of HIV-1 RNA under assay conditions: using mini-pool testing, pools ≥ 50 RNA copies per ml achieved ≥ 92 % sensitivity, whereas in the standard procedure, samples ≥ 207 RNA copies/ml achieved 100 % sensitivity. Moreover, the COBAS AmpliScreen™ HIV-1 Test, version 1.5 (Roche) is suitable for detecting prevailing HIV-1 variants.

Characterization of primary isolates of HIV type 1 CRF28_BF, CRF29_BF, and unique BF recombinants circulating in São Paulo, Brazil

We report for the first time the genetic and biological characterization of 10 HIV-1 primary isolates representing CRF28_BF and CRF29_BF together with additional unique BF recombinant forms (URFs) obtained by PBMC cocultivation. Recombination is an important factor promoting the increase in the genetic diversity of HIV-1. Notably, more than 20% of HIV-1 sequences worldwide were recombinants. Several recombinant viruses were reported in Brazil, and six circulating recombinant forms (CRFs) have been identified (CRF28_BF, CRF29_BF, CRF31_BC, CRF39_BF, CRF40_BF, and CRF46_BF). CRF28_BF and CRF29_BF were found to infect almost 30% of the patients in São Paulo State. The near full-length genomes of these 10 primary isolates were amplified by nested PCR in three overlapping segments, purified, and sequenced. Three samples were related to CRF28_BF, three to CRF29_BF, and four were unique recombinant forms (URFs), as determined by their breakpoint profile determined with the jpHMM program. Additionally, the coreceptor usage of these isolates was investigated in vitro using GHOST assays, which revealed three dual-tropic (X4/R5) viruses, four lymphotropic (X4) viruses, and three macrophage-tropic (R5) viruses with different V3-loop motifs, which challenges the notion that GWGR-carrying viruses are macrophage-tropic only. In sum, we report a much-anticipated well-characterized panel of viruses representing CRF28_BF, CRF29_BF, and URFs from São Paulo State, Brazil.

Interplay between HIV-1 and Host Genetic Variation: A Snapshot into Its Impact on AIDS and Therapy Response

As of February 2012, 50 circulating recombinant forms (CRFs) have been reported for HIV-1 while one CRF for HIV-2. Also according to HIV sequence compendium 2011, the HIV sequence database is replete with 414,398 sequences. The fact that there are CRFs, which are an amalgamation of sequences derived from six or more subtypes (CRF27_cpx (cpx refers to complex) is a mosaic with sequences from 6 different subtypes besides an unclassified fragment), serves as a testimony to the continual divergent evolution of the virus with its approximate 1% per year rate of evolution, and this phenomena per se poses tremendous challenge for vaccine development against HIV/AIDS, a devastating disease that has killed 1.8 million patients in 2010. Here, we explore the interaction between HIV-1 and host genetic variation in the context of HIV/AIDS and antiretroviral therapy response.

A clustering phenomenon among HCV-1a strains among patients coinfected with HIV from Buenos Aires, Argentina

The human immunodeficiency virus (HIV) and hepatitis C virus (HCV) share the same transmission routes which lead to high coinfection rates. Among HIV-infected individuals such rates reached 21% in Argentina, being HCV-1a the most predominant subtype. In this work, 25 HCV subtype 1a (HCV-1a) strains from Argentinean patients coinfected with HIV were studied based on E2 and NS5A sequences. Phylogenetic analyses indicated that 12 strains were highly related to each other, constituting a highly supported (posterior probability = 0.95) monophyletic group that we called "M." The remaining HCV strains (group dispersed or "D") were interspersed along the phylogenetic trees. When comparing both groups of HCV-1a, 10 amino acid differences were located in functional domains of E2 and NS5A proteins that appeared to affect eventually the peptides binding to MHC-I molecules thus favoring immune escape and contributing to the divergence of HCV genotypes. Bayesian coalescent analyses for HCV-1a cluster M isolates indicated that the time to the most recent common ancestor (tMRCA) overlaps with the age estimated recently for the HIV-BF epidemic in Argentina. Furthermore, the genomic characterization based on pol gene analysis from HIV viremic patients showed that most HIV isolates from patients coinfected with HCV-1a cluster M were BF recombinants with identical recombination patterns. In conclusion, these results suggest the presence of an HCV-1a monophyletic cluster with a potential HIV co-transmission by phylogenetic analyses.

The HIV-1 epidemic: low- to middle-income countries

Low- to middle-income countries bear the overwhelming burden of the human immunodeficiency virus type 1 (HIV-1) epidemic in terms of the numbers of their citizens living with HIV/AIDS (acquired immunodeficiency syndrome), the high degrees of viral diversity often involving multiple HIV-1 clades circulating within their populations, and the social and economic factors that compromise current control measures. Distinct epidemics have emerged in different geographical areas. These epidemics differ in their severity, the population groups they affect, their associated risk behaviors, and the viral strains that drive them. In addition to inflicting great human cost, the high burden of HIV infection has a major impact on the social and economic development of many low- to middle-income countries. Furthermore, the high degrees of viral diversity associated with multiclade HIV epidemics impacts viral diagnosis and pathogenicity and treatment and poses daunting challenges for effective vaccine development.

Near full-length sequence analysis of HIV type 1 BF recombinants from Italy

Recombination between HIV-1 subtypes B and F has generated several circulating and unique recombinant forms, particularly in Latin American areas. In Italy, subtype B is highly prevalent while subtype F is the most common pure non-B subtype. To investigate the recombination pattern in Italian BF recombinant viruses, we characterized full-length sequences derived from 15 adult patients, mostly Italian and infected by the heterosexual route. One of the BF mosaics was a CRF29, three sequences clustered with low bootstrap values with CRF39, CRF40, and CRF42. With the exception of the CRF29-like sequence, the other recombination patterns were unique, but two possible clusters were identified. Analysis of the gp120 V3 domain suggested a possible link with subtype F from Eastern Europe rather than from Latin America, favoring the hypothesis of local recombination between clade B and F viruses over that of import of BF recombinants from Latin America. HIV-1 subtypes B and F appear prone to generation of unique recombinants in Italy, warranting epidemiological surveillance and investigation of a possible clinical significance.

The Use of Bioinformatics for Studying HIV Evolutionary and Epidemiological History in South America

The South American human immunodeficiency virus type 1 (HIV-1) epidemic is driven by several subtypes (B, C, and F1) and circulating and unique recombinant forms derived from those subtypes. Those variants are heterogeneously distributed around the continent in a country-specific manner. Despite some inconsistencies mainly derived from sampling biases and analytical constrains, most of studies carried out in the area agreed in pointing out specificities in the evolutionary dynamics of the circulating HIV-1 lineages. In this paper, we covered the theoretical basis, and the application of bioinformatics methods to reconstruct the HIV spatial-temporal dynamics, unveiling relevant information to understand the origin, geographical dissemination and the current molecular scenario of the HIV epidemic in the continent, particularly in the countries of Southern Cone.

Molecular surveillance of HIV-1 in Madrid, Spain: a phylogeographic analysis

The molecular epidemiology of HIV-1 is constantly changing, mainly as a result of human migratory flows and the high adaptive ability of the virus. In recent years, Spain has become one of Europe's main destinations for immigrants and one of the western European countries with the highest rates of HIV-positive patients. Using a phylogeographic approach, we have analyzed the relationship between HIV-1 variants detected in immigrant and native populations of the urban area of Madrid. Our project was based on two coincidental facts. First, resistance tests were extended to naïve and newly diagnosed patients, and second, the Spanish government legislated the provision of legal status to many immigrants. This allowed us to obtain a large data set (n = 2,792) from 11 Madrid hospitals of viral pol sequences from the two populations, and with this unique material, we explored the impact of immigration in the epidemiological trends of HIV-1 variants circulating in the largest Spanish city. The prevalence of infections by non-B HIV-1 variants in the studied cohort was 9%, rising to 25% among native Spanish patients. Multiple transmission events involving different lineages and subsubtypes were observed in all the subtypes and recombinant forms studied. Our results also revealed strong social clustering among the most recent immigrant groups, such as Russians and Romanians, but not in those groups who have lived in Madrid for many years. Additionally, we document for the first time the presence of CRF47_BF and CRF38_BF in Europe, and a new BG recombinant form found in Spaniards and Africans is tentatively proposed. These results suggest that the HIV-1 epidemic will evolve toward a more complex epidemiological landscape.

Circulation of multiple patterns of unique recombinant forms B/CRF02_AG in France: precursor signs of the emergence of an upcoming CRF B/02

BACKGROUND

HIV-1 group M is characterized by substantial genetic diversity, and includes nine subtypes, more than 45 circulating recombinant forms (CRFs), and numerous unique recombinant forms (URFs). In France, the epidemic is characterized by predominance of subtype B strains, increasing prevalence of non-B subtypes (CRF02_AG being the most prevalent) and increasing at-risk behaviour in the MSM population. The high prevalence and co-circulation of B and CRF02_AG strains in this population raise the possibility that recombinant forms might emerge and spread.

METHODS

Samples from seven patients (five being MSM) were selected on the basis of subtyping discordances in different regions. The pattern of each near full-length genome of the viruses was characterized. The relationships between the newly and previously described B/CRF02_AG URFs were analysed using phylogenetic networks. Single genome amplification was used to search for the parental strains and confirmation of the breakpoints.

RESULTS

Seven unique recombination patterns were identified, breakpoints being found throughout the genomes, with hotspots in pol and accessory genes. No link was observed with the previous forms, but the CRF02 regions of two new viruses indicated that they are phylogenetically associated, suggesting a common ancestral strain. No evidence of circulating parental strains was found.

CONCLUSION

This description of seven URFs involving subtype B and CRF02_AG highlights the growing complexity of HIV molecular epidemiology in France. These multiple patterns, found mostly in MSM, and the hypothesis of a better fitness of some recombinant strains, argue for a context that could lead to the genesis of CRFB/02_AG strains in France.

Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors

HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment of env compartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizing in vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1 env intrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistence in vivo.

Identification of a new HIV type 1 BF intersubtype circulating recombinant form (CRF44_BF) in Chile

HIV-1 BF intersubtype recombinants are frequent in Argentina, Uruguay, and Brazil, where among a high diversity of BF unique recombinant forms (URFs), eight circulating recombinant forms (CRFs) have been characterized. Here, we describe a new one, designated CRF44_BF, identified in HIV-1 samples from Chile. In a previous report, where partial pol sequences of 136 HIV-1 infections of Chilean subjects were analyzed, a phylogenetic cluster of HIV-1 recombinant BF viruses from 10 individuals, with coincident intersubtype recombination points, was detected. One virus of this cluster had been characterized along its near full-length genome. A second one, from an epidemiologically unlinked HIV-1-infected subject, is described here. Both genomes share identical mosaic structures, consisting of a predominantly subtype F1 genome with three fragments of subtype B. Coincident breakpoints and phylogenetic clustering of the newly identified CRF44_BF with CRF12_BF, CRF17_BF, and CRF38_BF support a common origin of different CRF_BFs identified in Argentina, Uruguay, and Chile.

Phylodynamics of HIV-1 circulating recombinant forms 12_BF and 38_BF in Argentina and Uruguay

Background

Although HIV-1 CRF12_BF and CRF38_BF are two epidemiologically important recombinant lineages circulating in Argentina and Uruguay, little is known about their population dynamics.

Methods

A total of 120 "CRF12_BF-like" and 20 "CRF38_BF-like" pol recombinant sequences collected in Argentina and Uruguay from 1997 to 2009 were subjected to phylogenetic and Bayesian coalescent-based analyses to estimate evolutionary and demographic parameters.

Results

Phylogenetic analyses revealed that CRF12_BF viruses from Argentina and Uruguay constitute a single epidemic with multiple genetic exchanges among countries; whereas circulation of the CRF38_BF seems to be confined to Uruguay. The mean estimated substitution rate of CRF12_BF at pol gene (2.5 × 10-3 substitutions/site/year) was similar to that previously described for subtype B. According to our estimates, CRF12_BF and CRF38_BF originated at 1983 (1978-1988) and 1986 (1981-1990), respectively. After their emergence, the CRF12_BF and CRF38_BF epidemics seem to have experienced a period of rapid expansion with initial growth rates of around 1.2 year^-1 and 0.9 year^-1, respectively. Later, the rate of spread of these CRFs_BF seems to have slowed down since the mid-1990s.

Conclusions

Our results suggest that CRF12_BF and CRF38_BF viruses were generated during the 1980s, shortly after the estimated introduction of subtype F1 in South America (~1975-1980). After an initial phase of fast exponential expansion, the rate of spread of both CRFs_BF epidemics seems to have slowed down, thereby following a demographic pattern that resembles those previously reported for the HIV-1 epidemics in Brazil, USA, and Western Europe.

Young pregnant women living with HIV/AIDS in Criciuma, Southern Brazil, are infected almost exclusively with HIV type 1 clade C

Southern Brazil has the highest prevalence rate of AIDS in the country and is the only region in the Americas where HIV-1 C prevails. Metropolitan areas and harbor cities have been evaluated, but limited information is available for small towns and specific populations. We studied women attending the obstetric outpatient clinic of Criciuma, State of Santa Catarina in 2007 to evaluate the molecular epidemiology of HIV-1 among pregnant women living with HIV/AIDS. Forty-two cases had partial pol gene sequenced and additional partial gag and/or env genes from nine women. HIV subtyping was evaluated by phylogenetic methods and antiretroviral (ARV) drug resistance mutations (DRMs) at the Stanford Database. DRMs to one or more ARV class was observed in 20/42, 48% of cases, with 15/41, 37% with viral load <500 copies/ml. Subtype C at pol was identified in 33/42, 78.6% (95% CI: 64-89%), C mosaics (CB, CF) in 2, 4.8% (95% CI: 0.8-19%), F in 4, 9.5% (95% CI: 3-21%), and B in 3, 7.1% (95% CI: 1.8-18%). Discordance in concatenated gag/pol/env or intraregion mosaic was observed in 1/9, 11% of HIV-1 C genomes. The proportion of HIV-1 C in this study is the highest rate described in the Americas. Molecular surveillance in specific populations is instrumental for a better understanding of the Brazilian HIV epidemic.

Short communication: Evidences of recent decline in the expansion rate of the HIV type 1 subtype C and CRF31_BC epidemics in southern Brazil

The HIV-1 epidemic in southern Brazil is characterized by the high prevalence of subtype C and CRF31_BC infections but little is known about the population dynamics of these strains over time. We used a total of 82 env and 72 pol HIV-1 subtype C sequences collected from 1991 to 2006 and 47 pol CRF31_BC sequences collected from 1998 to 2006 from Brazilian patients to reconstruct the demographic history of these HIV-1 strains. Estimations of demographic history were performed using a Bayesian Markov Chain Monte Carlo coalescent-based approach as implemented in the BEAST program. Our analyses indicate that subtype C and CRF31_BC epidemics experienced an initial period of fast exponential spread in the southern Brazilian population during the 1980s and early 1990s, but the spreading rate of these epidemics seems to have slowed down since the middle 1990s. The initial mean exponential growth rate of the subtype C epidemic was estimated to be around 0.70-0.90/year, whereas the estimated population growth rate of CRF31_BC was 1.3/year, more than two times higher than that previously described for this CRF. These results suggest for the first time that the growth rate of subtype C and CRF31_BC epidemics has been changing over time in southern Brazil with evidence for a deceleration in recent years. During the expansion phase, the CRF31_BC seems to have spread at a rate much higher than Brazilian parental subtypes B and C.

Molecular characterization of the human immunodeficiency virus type 1 among children in Lima, Peru

In Peru, there is a lack of information on molecular analysis in pediatric human immunodeficiency virus (HIV) infection. At present, the mother-to-child transmission rate is estimated at approximately 2-4%. The objective of this study was to assess the molecular epidemiology of HIV-1 in infected children. Children with suspected or confirmed pulmonary tuberculosis were evaluated at two public hospitals between 2002 and 2007. Whole blood samples were obtained from 90 HIV-positive children, who were confirmed to be positive by enzyme-linked immunosorbent assay and Western blot. The specimens were subjected to envelope heteroduplex mobility assay (env HMA) followed by gag and pol gene region sequence analysis. Subtype B was found in 88 (98%) of 90 children and 2 (2%) children were subtype BF recombinants. This is the first report of recombinant HIV strains in HIV-infected children in Peru. Understanding the origin, diversity, and spread of HIV strains worldwide will be necessary for the development of an effective vaccine that targets pediatric populations throughout the world.

Short communication: Molecular characterization of HIV type 1 BF pol recombinants from São Paulo, Brazil

In the Brazilian HIV-1 epidemic, subtypes B, C, and F1 are cocirculating in the population. Sequences of the partial pol gene from 463 HIV-1-infected patients were obtained from plasma samples and viral subtype was characterized. BF recombinants were found in 8% of the samples. Fifteen different patterns were observed. A CRF28_BF and CRF29_BF structure was found in 29.7% of the samples, CRF12_BF in 13.5%, and CRF39_BF in 2.7%. Two other patterns were identified in each of three samples. These findings could indicate a new CRF description, but to determine this a full length study is required.

Recombination in feline immunodeficiency virus from feral and companion domestic cats

Background

Recombination is a relatively common phenomenon in retroviruses. We investigated recombination in Feline Immunodeficiency Virus from naturally-infected New Zealand domestic cats (Felis catus) by sequencing regions of the gag, pol and env genes.

Results

The occurrence of intragenic recombination was highest in env, with evidence of recombination in 6.4% (n = 156) of all cats. A further recombinant was identified in each of the gag (n = 48) and pol (n = 91) genes. Comparisons of phylogenetic trees across genes identified cases of incongruence, indicating intergenic recombination. Three (7.7%, n = 39) of these incongruencies were found to be significantly different using the Shimodaira-Hasegawa test.

Surprisingly, our phylogenies from the gag and pol genes showed that no New Zealand sequences group with reference subtype C sequences within intrasubtype pairwise distances. Indeed, we find one and two distinct unknown subtype groups in gag and pol, respectively. These observations cause us to speculate that these New Zealand FIV strains have undergone several recombination events between subtype A parent strains and undefined unknown subtype strains, similar to the evolutionary history hypothesised for HIV-1 "subtype E".

Endpoint dilution sequencing was used to confirm the consensus sequences of the putative recombinants and unknown subtype groups, providing evidence for the authenticity of these sequences. Endpoint dilution sequencing also resulted in the identification of a dual infection event in the env gene. In addition, an intrahost recombination event between variants of the same subtype in the pol gene was established. This is the first known example of naturally-occurring recombination in a cat with infection of the parent strains.

Conclusion

Evidence of intragenic recombination in the gag, pol and env regions, and complex intergenic recombination, of FIV from naturally-infected domestic cats in New Zealand was found. Strains of unknown subtype were identified in all three gene regions. These results have implications for the use of the current FIV vaccine in New Zealand.

Rates of evolutionary change in viruses: patterns and determinants

Understanding the factors that determine the rate at which genomes generate and fix mutations provides important insights into key evolutionary mechanisms. We review our current knowledge of the rates of mutation and substitution, as well as their determinants, in RNA viruses, DNA viruses and retroviruses. We show that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.

Chronology of the HIV-1 CRF07_BC expansion in East Asia

The HIV-1 epidemic among injecting drug users (IDU) in Taiwan is caused primarily by CRF07_BC infections. Evolutionary analyses, which utilize outgroup reference strains from northwestern China (Xinjiang), reveal that CRF07_BC was introduced into southern Taiwan in 1998-2001 and spread to central-northern Taiwan in 2001-2003, causing the largest HIV/AIDS epidemic in Taiwan. The separate introduction of CRF07_BC into Xinjiang occurred in 1992-1995. This study illustrates the temporal dynamics of CRF07_BC spread among IDU across east Asia.

Low Rate of Emergence of Nevirapine and Lamivudine Resistance after Post-Partum Interruption of a Triple-Drug Regimen

Introduction

Emergence of nevirapine (NVP) resistance may be a consequence of its use in monotherapy to prevent HIV mother-to-child transmission (MTCT). The aim of this study was to evaluate the emergence of strains resistant to NVP and lamivudine (3TC) after discontinuation of anti-retroviral therapy (ART) with 3TC/zidovudine (ZDV)/NVP.

Methods

Twenty pregnant women (ART-naive or pre-exposed only to ZDV), to whom 3TC/ZDV/NVP was prescribed as MTCT prophylaxis, were studied. They received ART for a median of 4 months with median viral load (VL) at labour <50 copies/ml. Samples were collected between 1 and 15 months (median: 3 months) after ART interruption. Sequence-selective real-time PCR (SPCR), which quantifies minority viral populations containing K103N, Y181C and M184V mutations, and standard genotypic sequencing were assayed.

Results

No mutations associated with resistance to 3TC or NVP were found by standard population sequencing. Analysis of K103N by SPCR showed that 35% of the patients contained ≤0.1% of viruses carrying either the AAC or AAT mutations. For Y181C mutation, 10% of the patients contained <0.5% of viruses with TGT codon change. For M184V mutation, one patient contained 6.2% of virus with GTG mutation and 13 patients (65%) contained <0.9% of mutated viruses. Four women were re-exposed to 3TC/ZDV/NVP and achieved HIV VL <50 copies/ml. No perinatal transmission occurred in any of the 22 births.

Conclusions

NVP associated with ZDV/3TC as a regimen to prevent MTCT may involve a low risk for the selection of antiretroviral-resistant strains and may not jeopardize the use of these same drugs for future treatment.

Description of the first full-length HIV type 1 subtype F1 strain in Argentina: implications for the origin and dispersion of this subtype in South America

HIV-1 subtype F1 in South America is mainly found as part of diverse BF1 recombinant forms and only five full-length "pure" F1 strains from Brazil were characterized to date. In the present study we describe the first near full-length sequence of a nonrecombinant F1 HIV-1 strain from Argentina, and explore the epidemiological history of this subtype in South America. Three separate phylogenetic analyses were carried out: with all available F1 full-length sequences, with concatenated F1 sequences contained in F1 and BF1 strains, and with partial F1 env sequences derived from worldwide strains. All analyses were consistent in showing a local origin of the newly reported Argentine subtype F1 strain, and a common ancestry of the South American subtype F1 sequences, present either in pure or recombinant genomes. By coalescent analysis, the onset date of the HIV-1 subtype F1 epidemic in South America was estimated to be around the late 1970s. The results indicate for the first time that nonrecombinant F1 HIV-1 strains are present in Argentina, and suggest that the subtype F1 epidemic in South America was initiated by the introduction of a very small group of genetically related viruses during late 1970s.