Phylogenetic analysis of HIV-1 transmission: pol gene sequences are insufficient to clarify true relationships between patient isolates

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

Background

Phylogenetic analyses of HIV sequences are used to detect clusters and inform public health interventions. Conventional approaches summarize within-host HIV diversity with a single consensus sequence per host of the pol gene, obtained from Sanger or next-generation sequencing (NGS). There is growing recognition that this approach discards potentially important information about within-host sequence variation, which can impact phylogenetic inference. However, whether alternative summary methods that incorporate intra-host variation impact phylogenetic inference of transmission network features is unknown.

Methods

We introduce profile sampling, a method to incorporate within-host NGS sequence diversity into phylogenetic HIV cluster inference. We compare this approach to Sanger- and NGS-derived pol and near-whole-genome consensus sequences and evaluate its potential benefits in identifying molecular clusters among all newly-HIV-diagnosed individuals over six months at the largest HIV center in Rhode Island.

Results

Profile sampling cluster inference demonstrated that within-host viral diversity impacts phylogenetic inference across individuals, and that consensus sequence approaches can obscure both magnitude and effect of these impacts. Clustering differed between Sanger- and NGS-derived consensus and profile sampling sequences, and across gene regions.

Discussion

Profile sampling can incorporate within-host HIV diversity captured by NGS into phylogenetic analyses. This additional information can improve robustness of cluster detection.

Factors influencing HIV-1 phylogenetic clustering

PURPOSE OF REVIEW

A major goal of public health in relation to HIV/AIDS is to prevent new transmissions in communities. Phylogenetic techniques have improved our understanding of the structure and dynamics of HIV transmissions. However, there is still no consensus about phylogenetic methodology, sampling coverage, gene target and/or minimum fragment size.

RECENT FINDINGS

Several studies use a combined methodology, which includes both a genetic or patristic distance cut-off and a branching support threshold to identify phylogenetic clusters. However, the choice about these thresholds remains an inherently subjective process, which affects the results of these studies. There is still a lack of consensus about the genomic region and the size of fragments that should be used, although there seems to be emerging a consensus that using longer segments, allied with the use of a realistic model of evolution and a codon alignment, increases the likelihood of inferring true transmission clusters. The pol gene is still the most used genomic region, but recent studies have suggested that whole genomes and/or sequences from nef and gp41 are also good targets for cluster reconstruction.

SUMMARY

The development and application of standard methodologies for phylogenetic clustering analysis will advance our understanding of factors associated with HIV transmission. This will lead to the design of more precise public health interventions.

Molecular linkage tracing of HIV-1 transmission events in seroconcordant couples in Guangxi Province, Southeastern China

Background

Guangxi Province in Southeastern China has one of the highest HIV-1 infection and transmission rates in stable couples. However, the mode of transmission at the molecular level has seldom been reported amongst this group. It is important to investigate this issue to support the treatment-as-prevention approach and for efficient interventions.

Methods

HIV-1 subgenomic regions (1.2 kb of pol and a 660-bp env C2V5 fragment) were sequenced in 42 couples. A couple linkage assessment was performed by phylogenetic analysis of sequences and Bayesian analysis of genetic distances. A subset of pairs was selected for single-genome amplification.

Results

Thirty-five pairs (83.3 %, 35/42) were identified as linked, 3 pairs (7.1 %, 3/42) were identified as indeterminate, and 4 pairs (9.5 %) were identified as unlinked. The predominant intra-couple-transmitted HIV-1 subtype was CRF01_AE (80 %, 28/35). The median genetic distance of linked couples was 0.5 %.

Conclusion

The majority of HIV-1 transmission events in this study occurred within the partnership, and the predominant HIV-1 subtype was CRF01_AE. Further research on the mode of HIV transmission in other locations is needed.

Electronic supplementary material

The online version of this article (doi:10.1186/s40064-016-3578-2) contains supplementary material, which is available to authorized users.

Phylogenetic and geospatial evaluation of HIV-1 subtype diversity at the largest HIV center in Rhode Island

Individuals infected with HIV-1 non-B subtypes are understudied in the United States. Their characterization may augment prevention and treatment interventions. We examined the regional molecular epidemiology of non-B subtypes using a combined phylogenetic and geospatial approach. HIV-1 pol sequences and clinical data obtained for routine clinical care were aggregated from 2004 to 2011 at the largest HIV center in Rhode Island. Subtyping was performed by neighbor-joining and maximum-likelihood phylogeny and compared across eight commonly used tools (HIVdb, REGA, RIP, NCBI, Geno2Pheno, EuResist, jpHMM and STAR) using proportional odds ordinal regression. Individuals with non-B subtypes were characterized according to demographics and risk factors for infection, intra-subtype clustering by maximum-likelihood phylogeny, and geospatial hotspot analysis using Getis-Ord Gi(∗) statistics. Of 1277 unique sequences, phylogenetic subtyping demonstrated 8.3% (N=106, 95% CI 6.8-10%) non-B subtypes and circulating recombinant forms (CRFs): CRF02_AG=46; A=15; C=15; CRF01_AE=6; CRF06_CPX=5; CRF14_BG=5; G=3; CRF43_02G=3; D=3; CRF24_BG=3; CRF11_CPX=1; F1=1. Compared to phylogeny, Geno2Pheno was the most concordant (86% exact match) followed by REGA (85%), EuResist (85%) and STAR (82%). Of 106 individuals with non-B subtypes, 50% were male, 71% acquired infection through heterosexual transmission; 76%, were born in Africa, 6% Southeast Asia, 5% the United States, 3% Central America, 1% Europe, and 9% unknown. Eighty percent of CRF02_AG, 93% of A and 87% of C sequences were from African-born individuals. Twenty-two percent of non-B subtypes formed transmission clusters, including a significant number of younger individuals with perinatally-acquired infection. Geospatial analyses revealed hotspots of B and non-B subtypes in the state capital with a more concentrated focus among non-B subtypes. Molecular examination of regional HIV diversity revealed a larger than expected non-subtype B infected population, mostly born in Africa, with low ongoing regional transmission. Phylogenetic and geospatial characterization of infection clusters is helpful to identify targets for treatment and prevention interventions.

Inferring the source of transmission with phylogenetic data

Identifying the source of transmission using pathogen genetic data is complicated by numerous biological, immunological, and behavioral factors. A large source of error arises when there is incomplete or sparse sampling of cases. Unsampled cases may act as either a common source of infection or as an intermediary in a transmission chain for hosts infected with genetically similar pathogens. It is difficult to quantify the probability of common source or intermediate transmission events, which has made it difficult to develop statistical tests to either confirm or deny putative transmission pairs with genetic data. We present a method to incorporate additional information about an infectious disease epidemic, such as incidence and prevalence of infection over time, to inform estimates of the probability that one sampled host is the direct source of infection of another host in a pathogen gene genealogy. These methods enable forensic applications, such as source-case attribution, for infectious disease epidemics with incomplete sampling, which is usually the case for high-morbidity community-acquired pathogens like HIV, Influenza and Dengue virus. These methods also enable epidemiological applications such as the identification of factors that increase the risk of transmission. We demonstrate these methods in the context of the HIV epidemic in Detroit, Michigan, and we evaluate the suitability of current sequence databases for forensic and epidemiological investigations. We find that currently available sequences collected for drug resistance testing of HIV are unlikely to be useful in most forensic investigations, but are useful for identifying transmission risk factors.

Molecular data from pathogens may be useful for identifying the source of infection and identifying pairs of individuals such that one host transmitted to the other. Inference of who acquired infection from whom is confounded by incomplete sampling, and given genetic data only, it is not possible to infer the direction of transmission in a transmission pair. Given additional information about an infectious disease epidemic, such as incidence of infection over time, and the proportion of hosts sampled, it is possible to correct for biases stemming from incomplete sampling of the infected host population. It may even be possible to infer the direction of transmission within a transmission pair if additional clinical, behavioral, and demographic covariates of the infected hosts are available. We consider the problem of identifying the source of infection using HIV sequence data collected for clinical purposes. We find that it is rarely possible to infer transmission pairs with high credibility, but such data may nevertheless be useful for epidemiological investigations and identifying risk factors for transmission.

Molecular epidemiology of HIV-1 transmission in a cohort of HIV-1 concordant heterosexual couples from Dakar, Senegal

Background

A large number of HIV-1 infections in Africa occur in married couples. The predominant direction of intracouple transmission and the principal external origins of infection remain important issues of debate.

Methods

We investigated HIV-1 transmission in 46 HIV-1 concordant positive couples from Dakar, Senegal. Intracouple transmission was confirmed by maximum-likelihood phylogenetic analysis and pairwise distance comparisons of HIV-1 env gp41 sequences from both partners. Standardized interview data were used to deduce the direction as well as the external sources of the intracouple transmissions.

Results

Conservative molecular analyses showed linked viruses in 34 (74%) couples, unlinked viruses in 6 (13%) couples, and indeterminate results for 6 (13%) couples. The interview data corresponded completely with the molecular analyses: all linked couples reported internal transmission and all unlinked couples reported external sources of infection. The majority of linked couples (93%) reported the husband as internal source of infection. These husbands most frequently (82%) reported an occasional sexual relationship as external source of infection. Pairwise comparisons of the CD4 count, antiretroviral therapy status, and the proportion of gp41 ambiguous base pairs within transmission pairs correlated with the reported order of infection events.

Conclusions

In this suburban Senegalese population, a majority of HIV-1 concordant couples showed linked HIV-1 transmission with the husband as likely index partner. Our data emphasize the risk of married women for acquiring HIV-1 as a result of the occasional sexual relationships of their husbands.

Short communication: Transmitted drug resistance and molecular epidemiology in antiretroviral naive HIV type 1-infected patients in Rhode Island

Transmission of HIV-1 drug resistance has important clinical and epidemiological consequences including earlier treatment failure and forward transmission of resistance strains in high-risk groups. To evaluate the prevalence and molecular epidemiology of transmitted drug resistance in Rhode Island, we collected genotypic, demographic, clinical, and laboratory data from treatment-naive individuals presenting to the largest outpatient HIV clinic in the state from January 2007 to November 2007. Sequences from 35 treatment-naive individuals were available, 83% of whom were men who had sex with men (MSM). All sequences were HIV-1 subtype B. Drug resistance mutations were identified in 7/35 [20%; 95% confidence interval (CI), 0.08-0.37] patients, six of whom had K103N. Two phylogenetic transmission clusters were found, involving 17% (6/35) of individuals, three in each cluster. We did not find an association between belonging to a cluster and age, gender, AIDS-defining illness, CD4 cell count, or viral load. Drug resistance mutations were more commonly observed in transmission clusters (p = 0.08). Individuals in one cluster all had K103N and were MSM who had attended local bathhouses. Individuals forming clusters were significantly more likely to have visited a bathhouse compared to nonclusters (p = 0.02). The prevalence of transmitted drug resistance in Rhode Island is high, further justifying genotypic testing on presentation to care and prior to treatment initiation. Molecular epidemiological analysis and association of resistance with phylogenetic networks using data obtained for clinical purposes may serve as useful tools for the prevention of drug resistance transmission and for contact tracing.

An uncommon case of HIV-1 transmission due to a knife fight

This article describes a case of human immunodeficiency virus type 1 (HIV-1) infection transmission caused by a bloody knife fight in a robbery. The victim was a 69-year-old man who was not infected with HIV-1, and his wife was HIV-antibody negative. A robber, a 42-year-old man, was HIV antibody-positive since December 2005 and had not taken antiretroviral therapy. The BED IgG Capture incidence EIA (BED-CEIA assay) data showed that the specimens from the victim were compatible with a recent seroconversion. Phylogenetic analysis of fragments of pol, encompassing protease and a portion of reverse transcriptase, and of env genes isolated from the victim, the robber, and a local population samples of HIV-1 positive individuals showed that the victim's HIV-1 sequences were most closely related to and nested within a lineage comprised of the robber's HIV-1 sequences. We provide HIV-1 seroconversion data and phylogenetic analysis as evidence that the HIV-1 transmission likely occurred from contact during the robbery.

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.

Short communication: Different mutation patterns in subtype CRF06_cpx after mother-to-child transmission

Abstract Development of drug resistance mutation patterns (DRMP) in HIV after treatment failure depends on the drugs used in the failing regimen. However, selected patterns may not be unique; there is evidence that selection of DRMP for nelfinavir is dependent on subtype and/or background polymorphisms. Here we describe the selection of DRMP in a mother and son infected with subtype CRF06_cpx by mother-to-child transmission. Four years after delivery the mother received stavudine/lamivudine/nelfinavir as first-line therapy. Genotypic resistance tests (GRT) during follow-up showed selection of M184V/L283I in reverse transcriptase (RT) and H63Q/A71V/L90M in protease (PR). The child started treatment 8 months after birth with stavudine/didanosine/nelfinavir followed by an intensification period with efavirenz. Due to toxicity, efavirenz was removed from the regimen again. GRT during follow-up showed selection of L74V/K103N/M184V/M230L in RT and M46I/H63Q/N88S in PR. The viral load (VL) of the mother was initially undetectable followed by intermediate replication (1000-21,000 copies/ml), whereas the child had both periods of undetectable VL and low-level replication. Although both patients were infected with the same virus and treated with the same protease inhibitor, different DRMPs were selected. Whether the nucleoside backbone, course of antiretroviral therapy, or different host environment is responsible for this variability must be determined in larger studies.

Seventeen-year-old mother-to-child HIV type 1 transmission identified by phylogeny and signature patterns

A case, in which the clinical suspicion of perinatal HIV transmission of a newly diagnosed 17-year-old woman was supported by the phylogenetic analyses of pol sequences obtained for routine resistance testing and further substantiated by analyses of gag and env, is described.

Is transmission of HIV-1 in non-viraemic serodiscordant couples possible?

Several studies have shown that HIV-1 transmission in serodiscordant couples is significantly reduced when the plasma viral load (pVL) in the infected partner is low or undetectable. However, residual infectivity in the seminal compartment despite undetectable pVL has also been shown. Here we report HIV-1 transmission in a serodiscordant couple despite successful antiretroviral therapy of the HIV-infected partner. The newly infected partner had a negative HIV-1 screening ELISA when his HIV-1- positive partner was already on antiretroviral treatment with undetectable pVL, which remained undetectable beyond the time of seroconversion in the initially negative partner. Frozen blood samples were analyzed phylogenetically from the HIV-1-positive patient and the newly infected partner before treatment and shortly after seroconversion, respectively; they showed a true relationship. On the basis of these data, the present report suggests that transmission of HIV-1 can occur despite undetectable pVL. This should be added to the discussion of prevention strategies, which should not advise the abandonment of safer-sex practices without referring to the relatively low but not impossible risk of HIV-1 transmission in this context.

Transmission of HIV-1 infection due to a fist fight

Summary

We report a case of HIV-1 infection transmission caused by a fist fight between brothers. A 30-year-old Caucasian UK resident man developed ‘flu-like illness with symptoms of lethargy and weakness. Persistent lymphadenopathy six months later lead to HIV antibody testing, which was positive. Of note, his 37-year-old brother, who was HIV antibody-positive since August 2000, was taking HAART (combivir and nevaripine) with CD4 350 × 106/L (16%) with viral load 4800 copies/mL (log 2.58). A bloody fight had occurred between them four weeks prior to onset of symptoms. Phylogenetic analysis was undertaken. Analysis of the pol gene region indicated that samples from both brothers belonged to the subtype C clade of HIV-1, and that the sequences were closely related to one another. Exposure risk data are extremely useful in helping counsel patients prior to HIV-testing but, as this case illustrates, does not cover all situations.

Identifying HIV-1 dual infections

Transmission of human immunodeficiency virus (HIV) is no exception to the phenomenon that a second, productive infection with another strain of the same virus is feasible. Experiments with RNA viruses have suggested that both coinfections (simultaneous infection with two strains of a virus) and superinfections (second infection after a specific immune response to the first infecting strain has developed) can result in increased fitness of the viral population. Concerns about dual infections with HIV are increasing. First, the frequent detection of superinfections seems to indicate that it will be difficult to develop a prophylactic vaccine. Second, HIV-1 superinfections have been associated with accelerated disease progression, although this is not true for all persons. In fact, superinfections have even been detected in persons controlling their HIV infections without antiretroviral therapy. Third, dual infections can give rise to recombinant viruses, which are increasingly found in the HIV-1 epidemic. Recombinants could have increased fitness over the parental strains, as in vitro models suggest, and could exhibit increased pathogenicity. Multiple drug resistant (MDR) strains could recombine to produce a pan-resistant, transmittable virus.

We will describe in this review what is presently known about super- and re-infection among ambient viral infections, as well as the first cases of HIV-1 superinfection, including HIV-1 triple infections. The clinical implications, the impact of the immune system, and the effect of anti-retroviral therapy will be covered, as will as the timing of HIV superinfection. The methods used to detect HIV-1 dual infections will be discussed in detail. To increase the likelihood of detecting a dual HIV-1 infection, pre-selection of patients can be done by serotyping, heteroduplex mobility assays (HMA), counting the degenerate base codes in the HIV-1 genotyping sequence, or surveying unexpected increases in the viral load during follow-up. The actual demonstration of dual infections involves a great deal of additional research to completely characterize the patient's viral quasispecies. The identification of a source partner would of course confirm the authenticity of the second infection.

Genetic diversity of HIV-1 non-B strains in Sicily: evidence of intersubtype recombinants by sequence analysis of gag, pol, and env genes

The molecular epidemiology of HIV-1 strains in Sicily (Italy) was phylogenetically investigated by the analysis of HIV-1 gag, pol, and env gene sequences from 11 HIV-1 non-B strains from 408 HIV-1-seropositive patients observed from September 2001 to August 2006. Sequences suggestive of recombination were further investigated by bootscanning analysis of various fragments. Overall, we identified several second-generation recombinant (SGRs) strains, which contained genetic material of CRF02_AG in at least one gene. Notably, three individuals were found to be infected with subsubtype A3, and one of them showed genetic recombination with subsubtype A4. The current study emphasizes the genetic analysis of gag, pol, and env genes as a powerful tool to trace the spread of complex HIV-1 recombinant forms, and highlight the genetic diversity of HIV-1 non-B strains in Italy.

Introduction of HIV type 1 into an isolated population: molecular epidemiologic study from Greenland

Introduction of HIV-1 into a population may not always give rise to a subsequent epidemic. Greenland is an isolated and sparsely populated island in The Danish Kingdom. We aimed to estimate the number of introductions of HIV-1 into Greenland, the number of subsequent epidemics, and the countries from which the virus was introduced. Phylogenetic analyses were performed on three regions of HIV-1 (gag, pol, and env) in samples from 70 Greenlandic patients. Furthermore, we included gene sequences from contemporary Danish HIV-1-infected patients and sequences from the Los Alamos HIV Sequence Database. All Greenlandic sequences were subtype B except one sequence found to be a recombinant (probably CRF13). Sequence clusters in the phylogenetic trees indicated that there had been at least nine introductions of HIV-1 into Greenland. One cluster, supported by bootstrap values of 81, 76, and 96% for gag, pol, and env, corresponding to one introduction, contained 53 (76%) of the Greenland patients. The patients in the cluster differed from other Greenlandic patients in epidemiological parameters. Two distinct subgroups within the main cluster were concentrated around the two largest Greenlandic towns. Although HIV-1 has been introduced into Greenland at least nine times, only one introduction gave rise to an epidemic. The phylogeny did not indicate from where the main Greenland cluster had been introduced as no database sequence from outside Greenland was genetically close to this cluster. The large diversity between the main Greenland cluster and the rest of the sequences is most likely due to a founder effect.

Evaluation of an in-house genotyping resistance test for HIV-1 drug resistance interpretation and genotyping

INTRODUCTION

The human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) has been considered essential for HIV-1 drug resistance monitoring. However, it is not commonly used in some developing countries in Asia and Africa due to its high running cost.

OBJECTIVE

This study aims to evaluate a new low-cost in-house GRT for both subtype B and non-B HIV-1.

STUDY DESIGN

The in-house GRT sequenced the entire protease and 410 codons of reverse transcriptase (RT) in the pol gene. Its performance on drug resistance interpretation was evaluated against the FDA-approved ViroSeq HIV-1 Genotyping System. Particularly, a panel of 235 plasma samples from 205 HIV-1-infected patients in Hong Kong was investigated. The HIV-1 drug resistance-related mutations detected by the two systems were compared. The HIV-1 subtypes were analyzed through the REGA HIV-1 Genotyping Tool and env phylogenetic analysis.

RESULTS

Among the 235 samples, 229 (97.4%) were successfully amplified by both in-house and ViroSeq systems. All PCR-negative samples harbored viral RNA at <400 copies/mL. The in-house and ViroSeq system showed identical drug resistance-related mutation patterns in 216 out of 229 samples (94.3%). The REGA pol genotyping results showed 93.9% (215/229) concordance with the env phylogenetic results including HIV-1 subtype A1, B, C, D, G, CRF01_AE, CRF02_AG, CRF06_cpx, CRF07_BC, CRF08_BC, CRF15_01B and other recombinant strains. The cost of running the in-house GRT is only 25% of that for the commercial system, thus making it suitable for the developing countries in Asia and Africa.

CONCLUSIONS

Overall, our in-house GRT provided comparable results to those of the commercial ViroSeq genotyping system on diversified HIV-1 subtypes at a more affordable price which make it suitable for HIV-1 monitoring in developing countries.

Molecular epidemiology of HIV-1 infection in a small Brazilian county: usefulness of envelope and polymerase sequences to epidemiologic studies

OBJECTIVE

The AIDS epidemic in Brazil is spreading from the large urban centers to small counties and the innermost parts of the country; however, data on the features of HIV-1 infection in these places are scarce. To study the routes of HIV-1 spread and assess the existence of transmission networks in such a setting, we performed a genetic analysis of viral sequences from the small county of Miracema, Rio de Janeiro State.

METHODS

HIV-1 envelope and polymerase sequences recovered from 63 adult patients (from a cohort of 78 patients) were phylogenetically analyzed.

RESULTS

A polyphyletic pattern ensued. Six clusters of sequences sharing close genetic relatedness were also recovered from 29 (46%) patients. Envelope and polymerase phylogenies yielded essentially the same results.

CONCLUSIONS

The polyphyletic pattern suggests multiple viral introductions in the region. Intracluster cases, including those with no known direct epidemiologic link, probably took part in the same chain of viral transmission. Such a pattern suggests the existence of sexual networks and the emergence of multiple new infections within a relatively short period, a potential molecular marker of high incidence.