The epidemic origin and molecular properties of B': a founder strain of the HIV-1 transmission in Asia

Exploring HIV-1 Transmission Features Among Older Individuals in Developed Eastern China

The number of newly reported HIV-1 infections among older individuals (≥50 years of age) has increased rapidly in Hangzhou, a central city in the Yangtze River Delta region of China. To provide a scientific basis for prevention and intervention strategies targeted at older individuals in Hangzhou, an epidemiological survey combined with molecular transmission network analysis was conducted. A total of 2,899 individuals with newly confirmed HIV-1 infections, including 635 older individuals and 2,264 younger individuals (<50 years of age), were enrolled in this study. Among older individuals, heterosexual contact was the predominant mode of HIV-1 transmission. In addition, it was observed that older individuals with lower levels of education exhibited a higher susceptibility to HIV-1 infection. The analysis of transmission network, which was inferred using HIV-TRACE algorithm, revealed that the newly diagnosed HIV-1 infections among older individuals in Hangzhou exhibited a pattern of scattered transmission, with key clusters primarily located in non-main urban areas. The predominant mode of transmission in these areas was nonmarital and noncommercial or nonmarital and commercial heterosexual transmission. Notably, the study highlighted a significant proportion of older individuals (73.3%, 11/15) within B subtype. Multivariate logistic regression analysis further revealed that the subtype B was a significant factor associated with older individuals having ≥3 node degrees in the network, occurring 5.55 times more frequent than subtype CRF07_BC (95% confidence intervals = 1.17-26.22, p = .031). Furthermore, the lower CD4 levels observed among older individuals underscored the challenge of late diagnosis in Hangzhou. Taken together, it is imperative to test and intervene for high-risk older individuals. To tackle this issue effectively, it is essential to enhance the detection of the B subtype and implement targeted interventions in key clusters within non-main urban areas. In addition, proactive measures should be implemented to address the challenge of late diagnosis in Hangzhou by promoting widespread testing among the older individuals, particularly in priority areas.

The characteristics of HIV-1 subtype B on phylogenetic dynamic and molecular transmission network in Fuyang City, China, 2011 to 2019

Introduction

HIV-1 subtype B, as once one of the earliest strains introduced into mainland China rapidly spread in commercial plasma donors and heterosexuals in 1990s. Here, we aim to investigate the origin and evolutionary history of HIV-1 subtype B in Fuyang city, China.

Methods

We collected sequences tested from Fuyang in the east of China where higher prevalence of HIV-1 among commercial plasma donors and heterosexuals to construct a phylogenetic tree using the Markov chain Monte Carlo (MCMC) algorithm, infer molecular transmission network using TN93 model and visualize it with Cytoscape software.

Results and discussion

Our results showed that >99% of subtype B sequences belonged to Thai B. The sequences from Fuyang often cluster closer to those from other its adjacent cities, which clustered together and formed a monophyletic cluster. HIV-1 B circulating in Fuyang dates back to approximately 1990. Among the 1,437 sequences, 166 clustered at a genetic distance of ≤1.2%, resulting in 73 clusters. The degree of clustering with at least one other person was 11.55%. Among the transmission clusters, 50 (80.65%) comprised two individuals. Most clusters consisted of both heterosexual transmission routes and men who have sex with men. Phylogenetic and molecular network analyses revealed a common origin with neighboring regions in mainland China, local onwards transmission after its introduction, and a limited clustering degree. However, at least two co-existing transmission routes in most transmission clusters imply a greater challenge in controlling the spread of HIV-1. Our findings highlight the value on tailoring prevention interventions by combination of molecular surveillance and epidemiology.

Consistency of spatial dynamics of HIV-1 and HCV among HIV-1/HCV coinfected drug users in China

BACKGROUND

As the transmission routes of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) are similar, previous studies based on separate research on HIV-1 and HCV assumed a similar transmission pattern. However, few studies have focused on the possible correlation of the spatial dynamics of HIV-1 and HCV among HIV-1/HCV coinfected patients.

METHODS

A total of 310 HIV-1/HCV coinfected drug users were recruited in Yingjiang and Kaiyuan prefectures, Yunnan Province, China. HIV-1 env, p17, pol and HCV C/E2, NS5B fragments were amplified and sequenced from serum samples. The genetic characteristics and spatial dynamics of HIV-1 and HCV were explored by phylogenetic, bootscanning, and phylogeographic analyses.

RESULTS

Among HIV-1/HCV coinfected drug users, eight HCV subtypes (1a, 1b, 3a, 3b, 6a, 6n, 6v, and 6u) and two HIV-1 subtypes (subtype B and subtype C), three HIV-1 circulating recombinant forms (CRF01_AE, CRF07_BC and CRF08_BC), and four unique recombinant forms (URF_BC, URF_01B, URF_01C and URF_01BC) were identified. HCV subtype 3b was the most predominant subtype in both Yingjiang and Kaiyuan prefectures. The dominant circulating HIV-1 subtypes for drug users among the two areas were CRF08_BC and URF_BC. Maximum clade credibility trees revealed that both HIV-1 and HCV were transmitted from Yingjiang to Kaiyuan.

CONCLUSIONS

The spatial dynamics of HIV-1 and HCV among HIV-1/HCV coinfected drug users seem to have high consistency, providing theoretical evidence for the prevention of HIV-1 and HCV simultaneously.

Impact of Adverse Childhood Events on the Psychosocial Functioning of Children Affected by Parental HIV in Rural China

Introduction: Children affected by parental HIV are more likely than unaffected peers to experience trauma and are at-risk for negative psychological and social outcomes. This study aimed to examine the relationship between adverse childhood events and psychosocial functioning among children affected by parental HIV. Methods: A total of 790 children ages 6-17 from Henan, China were enrolled in a longitudinal, randomized controlled trial of a resilience-based psychosocial intervention. At baseline, children reported on numerous psychosocial factors, including trauma exposure, symptoms of anxiety and depression, and peer social functioning. We used linear regression analysis to test the direct effect of trauma exposure on peer social functioning. We then tested whether depression and anxiety symptoms served as two potential parallel mediators in the association between trauma exposure and peer social functioning. Results: Trauma exposure was significantly associated with poor peer social functioning (β = -0.10, p = 0.005) when controlling for key covariates. When depression and anxiety symptoms were added to the model, the association between trauma exposure and peer social functioning became nonsignificant. Instead, there were significant indirect effects from trauma exposure to peer social functioning via depression (β = -0.06, 95%CI[-0.09, -0.03]) and anxiety (β = -0.02, 95%CI[-0.04, -0.00]). Conclusion: This study is among the first to link trauma exposure to peer social functioning deficits for children affected by parental HIV and demonstrates that symptoms of anxiety and depression mediate this relationship. Findings underscore the need for comprehensive psychosocial support for children affected by HIV, including screening for trauma exposure and mental health disorders.

Laos is Affected by HIV CRF01_AE and the Newly Identified CRF97_01B

Laos is the only landlocked country in Southeast Asia and borders Thailand, Myanmar and Cambodia, the three countries in this region that have been hardest hit by human immunodeficiency virus (HIV). Laos has been regarded as a low-HIV-prevalence country for decades. To understand the status of HIV in Laos in recent years, a retrospective study was performed among 2851 patients visiting a hospital in Vientiane, the capital of Laos, from November 2011 to May 2012. Whole blood samples were obtained from the patients, and DNA was extracted. HIV status was determined by HIV gag fragment-specific PCR assay. Sixty-nine samples were detected as HIV proviral DNA positive with a positive rate of 2.4% (69/2851). Sixty-one near full-length genomic sequences were obtained from the positive samples. The results of phylogenetic analysis showed that the vast majority (91.8%) of the HIV strains belonged to CRF01_AE, and the other five (8.2%) strains were identified as a new HIV circulating recombinant form CRF97_01B, which had a CRF01_AE backbone with an insertion of subtype B in the gag-pol region. Phylogeographic analysis revealed that HIV CRF01_AE circulating in Laos were multiply introduced from Thailand. These results indicated that Laos might be suffering a considerably more serious impact of HIV than previously believed. To keep this country from undergoing the same increase in HIV prevalence observed in its neighbors, immediate intervention measures and sufficient epidemiological research are urgently needed.

Prevalence of acquired drug resistance mutations in antiretroviral- experiencing subjects from 2012 to 2017 in Hunan Province of central South China

BACKGROUND

There are few data on the prevalence of acquired drug resistance mutations (ADRs) in Hunan Province, China, that could affect the effectiveness of antiretroviral therapy (ART).

OBJECTIVES

The main objectives of this study were to determine the prevalence of acquired drug resistance (ADR) the epidemic characteristics of HIV-1-resistant strains among ART-failed HIV patients in Hunan Province, China.

METHODS

ART-experienced and virus suppression failure subjects in Hunan between 2012 and 2017 were evaluated by genotyping analysis and mutations were scored using the HIVdb.stanford.edu algorithm to infer drug susceptibility.

RESULTS

The prevalence of HIV-1 ADR were 2.76, 2.30, 2.98, 2.62, 2.23and 2.17%, respectively, from 2012 to 2017. Overall 2295 sequences were completed from 2932 ART-failure patients, and 914 of these sequences were found to have drug resistance mutation. The most common subtype was AE (64.14%), followed by BC (17.91%) and B (11.50%). Among those 914 patients with drug resistance mutations,93.11% had NNRTI-associated drug resistance mutations, 74.40% had NRTI drug resistance mutations (DRMs) and 6.89% had PI DRMs. Dual-class mutations were observed in 591 (64.66%) cases, and triple-class mutations were observed in 43 (4.70%) cases. M184V (62.04%), K103N (41.90%) and I54L (3.83%) were the most common observed mutations, respectively, in NRTI-, NNRTI- and PI-associated drug resistance. 93.76% subjects who had DRMs received the ART first-line regimens. CD4 count, symptoms in the past 3 months, and ART adherence were found to be associated with HIV-1 DR.

CONCLUSIONS

This study showed that although the prevalence of HIV-acquired resistance in Hunan Province is at a low-level, the long-term and continuous surveillance of HIV ADR in antiretroviral drugs (ARVs) patients is necessary.

High rates of tenofovir failure in a CRF01_AE-predominant HIV epidemic in the Philippines

BACKGROUND

The Philippines has the fastest growing HIV epidemic in the Asia-Pacific. This increase was accompanied by a shift in the predominant HIV subtype from B to CRF01_AE. Increasing evidence points to a difference in treatment responses between subtypes. We examined treatment failure and acquired drug resistance (ADR) in people living with HIV (PLHIVs) after one year on antiretrovirals (ARVs).

METHODS

PLHIV maintained on ARVs for one year were recruited. Treatment failure was defined as a viral load of ≥1000 copies/mL. Sanger sequencing for genotyping and drug resistance mutation (DRM) detection was performed on patients failing treatment.

RESULTS

513 PLHIV were enrolled. The most common antiretroviral regimens were TDF+3TC + EFV (269) and AZT+3TC + EFV (155). 53 (10.3%) subjects failed treatment. Among these, 48 (90.6%) had DRMs, 84.9% were subtype CRF01_AE. Tenofovir-based regimens performed worse than zidovudine-based regimens (OR 3.28, 95% CI 1.58-7.52 p < 0.001). Higher rates of NRTI, NNRTI, K65R tenofovir resistance, and multi-class resistance were found compared to those reported in literature.

CONCLUSIONS

HIV treatment failure at one year of treatment in the Philippines is 10.3%. We found unusually high tenofovir and multiclass resistance, and optimal ARV regimens may need to be reevaluated for CRF01_AE-predominant epidemics.

Stigma and psychosocial wellbeing among children affected by parental HIV in China

OBJECTIVES

Parental HIV infection presents unique psychosocial challenges for families. Affected children are vulnerable to stigma-related distress from a parent's HIV status and are more likely to experience symptoms of depression and low self-esteem than unaffected peers. This study examined whether HIV-related stigma predicted poorer mental health among children affected by parental HIV and whether psychosocial assets mediated this relationship.

METHODS

A sample of 790 children (ages 6-17) affected by parental HIV in Henan, China reported on HIV-related stigma, social support, emotional regulation, future outlook, and mental health symptoms. Structural equation modeling was used to examine the direct and indirect effects of stigma on mental health.

RESULTS

Results indicated that stigma was associated with psychosocial resources, which in turn were associated with mental health symptoms. The indirect pathways from stigma to mental health symptoms through psychosocial resources were consistent across age and gender.

CONCLUSION

The experience of HIV-related stigma was associated with poorer overall mental health among children affected by parental HIV in China. Children's psychosocial resources, including social support, emotional regulation, and future outlook, mediated the relationship between HIV-related stigma and mental health symptoms. Future interventions may wish to target these modifiable aspects of wellbeing to improve social and behavioral outcomes in this vulnerable population.

A cluster randomized controlled trial to evaluate a resilience-based intervention for caregivers of HIV-affected children in China

OBJECTIVES

The Child-Caregiver-Advocacy Resilience (ChildCARE) intervention aims to enhance the psychosocial wellbeing of children affected by parental HIV by providing programing at three levels: child, caregiver, and community. The objective of the current study was to evaluate the intervention's efficacy in improving mental health and parenting outcomes for participating caregivers.

DESIGN

A cluster randomized controlled trial was used to evaluate initial efficacy of the intervention.

METHODS

A total of 790 caregivers of children affected by parental HIV were recruited from Henan, China. Caregivers and their children were randomly assigned to one-of-four intervention arms (control, child-only, child + caregiver, child + caregiver + community) to evaluate the multiple components of ChildCARE. Those assigned to receive the caregiver intervention participated in five 2-h intervention sessions designed to improve their parenting skills and enhance their ability to cope with daily stressors. Caregivers reported on their mental health and parenting behaviors at baseline, 12, 24, and 36 months, with mixed effect modeling used to examine intervention effects.

RESULTS

Caregivers who participated in the intervention reported decreased anxiety and parental stress at 12 months (P < 0.05). Participants also reported increased use of structured parenting skills (i.e., parental demandingness) at 12 and 24 months (P < 0.05). However, by 36 months, they reported significantly lower levels of parental competence (P < 0.01) than those assigned to the control condition.

CONCLUSION

Preliminary findings suggest that the caregiving component of ChildCARE yields initial improvements in some key parenting and mental health outcomes. However, the challenges of caring for children affected by HIV are complex and may require more intensive intervention to yield marked, positive changes across key caregiver outcomes.

Comparison of the genotypic and phenotypic properties of HIV-1 standard subtype B and subtype B/B' env molecular clones derived from infections in China

Although a number of standardized human immunodeficiency virus 1 (HIV-1) pseudoviruses have been generated to assess neutralizing antibodies, subtype B/B' has not been comprehensively characterized either genotypically or phenotypically. Full-length env genes were isolated from plasma samples derived from B/B'-infected individuals, including former plasma donors and men who had sex with men. The neutralization properties of these pseudoviruses were determined by testing against sCD4, 16 neutralizing monoclonal antibodies and 44 plasma samples, including samples from those infected with the three major prevalent clades in China. Twenty-eight pseudoviruses were successfully constructed, including 15 B' and 13 B strains. Compared with subtype B strains from North America and Europe, the B' strains from China showed greater variation in the V3 loop and higher susceptibility to the neutralizing antibody 2F5 and B/B' plasma samples. The B' strains from China showed significantly lower susceptibility to some trimer apex-binding neutralizing antibodies (PGT145, CH01, CH02, CH03, and CH04) than the B strains from Western countries. The 28 B-pseudotyped and B'-pseudotyped viruses were grouped into high, medium, and low clusters based on their overall neutralization sensitivity to plasma samples. The different genotypic and phenotypic properties of the standard subtype B from those of the Western viruses compared to the B and B' strains from China suggest that clones from HIV-1-infected individuals in China are more suitable for the evaluation of candidate vaccines targeting the subtype B/B' viruses circulating in China.

Phylodynamics of major CRF01_AE epidemic clusters circulating in mainland of China

As the most dominant HIV-1 strain in China, CRF01_AE needs to have its evolutionary and demographic history documented. In this study, we provide phylogenetic analysis of all CRF01_AE pol sequences identified in mainland China. CRF01_AE sequences were collected from the Los Alamos HIV Sequence Database and the local Chinese provincial centers of disease control and prevention. Phylogenetic trees were constructed to identify major epidemic clusters. Bayesian coalescent-based method was used to reconstruct the time scale and demographic history. There were 2965 CRF01_AE sequences from 24 Chinese provinces that were collected, and 5 major epidemic clusters containing 85% of the total CRF01_AE sequences were identified. Every cluster contains sequences from more than 10 provinces with 1 or 2 dominant transmission routes. One cluster arose in the 1990s and 4 clusters arose in the 2000s. Cluster I is in the decline stage, while the other clusters are in the stable stage. Obvious lineage can be observed among sequences from the same transmission route but not the same area. Two large clusters in high-level prevalence were found in MSM (Men who have sex with men), which highlighted that more emphasis should be placed on MSM for HIV control in mainland China.

Molecular Epidemiology of Human Immunodeficiency Virus

During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea.

Near Full-Length Genome Sequences of Two Novel HIV-1 Recombinant Forms Detected in Henan Province, China

In recent years, the population infected through sexual contact has seen the fastest growing prevalence of HIV transmission in Henan province, China. Here, we report two novel human immunodeficiency virus type 1 (HIV-1) recombinant form detected from a comprehensive HIV-1 molecular epidemiologic study among heterosexuals. Recombinant analyses of the near full-length genome of the two novel HIV-1 recombinant isolates: 01B.CN.2012.11092 was CRF01_AE that was partly replaced by a subtype B' fragment of 414 bp (from 4482-4896 according to the HXB2 calibrator). 01BC.CN.2011.11312 was composed of three segments (CRF01_AE/CRF_07BC/B') with breakpoints 4274 and 4833 according to the HXB2 calibrator. They are different from previously identified recombinant strains reported in China.

The application of HIV molecular epidemiology to public health

HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.

Overview of HIV molecular epidemiology among people who inject drugs in Europe and Asia

HIV strains continuously evolve, tend to recombine, and new circulating variants are being discovered. Novel strains complicate efforts to develop a vaccine against HIV and may exhibit higher transmission efficiency and virulence, and elevated resistance to antiretroviral agents. The United Nations Joint Programme on HIV/AIDS (UNAIDS) set an ambitious goal to end HIV as a public health threat by 2030 through comprehensive strategies that include epidemiological input as the first step of the process. In this context, molecular epidemiology becomes invaluable as it captures trends in HIV evolution rates that shape epidemiological pictures across several geographical areas. This review briefly summarizes the molecular epidemiology of HIV among people who inject drugs (PWID) in Europe and Asia. Following high transmission rates of subtype G and CRF14_BG among PWID in Portugal and Spain, two European countries, Greece and Romania, experienced recent HIV outbreaks in PWID that consisted of multiple transmission clusters including subtypes B, A, F1, and recombinants CRF14_BG and CRF35_AD. The latter was first identified in Afghanistan. Russia, Ukraine, and other Former Soviet Union (FSU) states are still facing the devastating effects of epidemics in PWID produced by A_FSU (also known as IDU-A), B_FSU (known as IDU-B), and CRF03_AB. In Asia, CRF01_AE and subtype B (Western B and Thai B) travelled from PWID in Thailand to neighboring countries. Recombination hotspots in South China, Northern Myanmar, and Malaysia have been generating several intersubtype and inter-CRF recombinants (e.g. CRF07_BC, CRF08_BC, CRF33_01B etc.), increasing the complexity of HIV molecular patterns.

HIV-1 subtype B: Traces of a pandemic

Human migration is a major process that shaped the origin and dissemination of HIV. Within HIV-1, subtype B (HIV-1B) is the most disseminated variant and it is assumed to be the causative agent in approximately 11% of all cases of HIV worldwide. Phylogenetic studies have revealed that HIV-1B emerged in Kinshasa (Africa) and was introduced into the Caribbean region via Haiti in or around 1966 by human migration. After localized dispersion, the virus was brought to the United States of America via homosexual/bisexual contact around 1969. Inside USA, the incidence of HIV-1B infection increased exponentially and it became established in the population, affecting not only homosexual individuals but also heterosexual individuals and injecting drug users. Soon after, the virus was disseminated and became established in other regions, including Europe, Asia, Latin America, and Australia. Recent studies suggest that, in addition to this pandemic clade, several lineages have emerged from Haiti and reached other Caribbean and Latin American countries via short-distance dissemination. Different subtype B genetic variants have also been detected in these epidemics. Four genetic variants have been described to date: subtype B', which mainly circulates in Thailand and other Asian countries; a specific variant mainly found in Trinidad and Tobago; the GPGS variant, which is primarily detected in Korea; and the GWGR variant, which is mainly detected in Brazil. This paper reviews the evolution of HIV-1B and its impact on the human population.

HIV-1 Thai B strain has spread out of former plasma donors into general population through sexual contact in Henan, China

Henan, China is characterized by the outbreak of HIV epidemic of Thai B strain in former plasma donors in 1990s. After the forbidden of paid blood donation, whether Thai B strain will spread out of former plasma donors into sexual transmitted population is unknown. To answer the question, phylogenetic analysis was used to explore relationships of HIV strains circulating in those two populations in the study. HIV-1 sero-positive drug-naïve patients infected through sexual contact were enrolled into the study. Full length gag and pol genes were amplified with nested RT-PCR followed by sequencing and phylogenetic analysis. The genotypes of anti-HIV drug resistance were also analyzed with available pol genes. HIV subtypes were determined in 249 individuals from 288 participants. Subtype B was dominant (202/249, 81.1%), followed by CRF01_AE (25/249, 10.0%), CRF07_BC (14/249, 5.6%), C (4/249, 1.6%), URF (3/249, 1.2%), and CRF08_BC (1/249, 0.4%). Most of subtype B strains belong to Thailand B lineage. All of Thai B strains identified in sexual transmitted population intermixed with those from former blood donors in phylogenetic tree, suggesting close phylogenetic relationship between strains epidemic in those two populations. TDR was identified in 9.9% individuals. Thai B strain has spread out of former blood donors in Henan province. The finding will contribute to understanding the distribution and evolution of HIV-1 in Henan province and also provide clue to behavior change intervention.

Co-infections and transmission networks of HCV, HIV-1 and HPgV among people who inject drugs

Co-infections with human immunodeficiency virus type 1 (HIV-1) and human pegivirus (HPgV) are common in hepatitis C virus (HCV)-infected individuals. However, analysis on the evolutionary dynamics and transmission network profiles of these viruses among individuals with multiple infections remains limited. A total of 228 injecting drug users (IDUs), either HCV- and/or HIV-1-infected, were recruited in Kuala Lumpur, Malaysia. HCV, HIV-1 and HPgV genes were sequenced, with epidemic growth rates assessed by the Bayesian coalescent method. Based on the sequence data, mono-, dual- and triple-infection were detected in 38.8%, 40.6% and 20.6% of the subjects, respectively. Fifteen transmission networks involving HCV (subtype 1a, 1b, 3a and 3b), HIV-1 (CRF33_01B) and HPgV (genotype 2) were identified and characterized. Genealogical estimates indicated that the predominant HCV, HIV-1 and HPgV genotypes were introduced into the IDUs population through multiple sub-epidemics that emerged as early as 1950s (HCV), 1980s (HIV-1) and 1990s (HPgV). By determining the difference in divergence times between viral lineages (ΔtMRCA), we also showed that the frequency of viral co-transmission is low among these IDUs. Despite increased access to therapy and other harm reduction interventions, the continuous emergence and coexistence of new transmission networks suggest persistent multiple viral transmissions among IDUs.

Evolutionary Dynamics of Tat in HIV-1 Subtypes B and C

Evolutionary characteristics of HIV-1 have mostly studied focusing its structural genes, Gag, Pol and Env. However, regarding the process of HIV-1's evolution, few studies emphasize on genetic changes in regulatory proteins. Here we investigate the evolutionary dynamics of HIV-1, targeting one of its important regulatory proteins, Tat. We performed a phylogenetic analysis and employed a Bayesian coalescent-based approach using the BEAST package to investigate the evolutionary changes in Tat over time in the process of HIV-1 evolution. HIV-1 sequences of subtypes B and C from different parts of the world were obtained from the Los Alamos database. The mean estimated nucleotide substitution rates for Tat in HIV-1 subtypes B and C were 1.53x10^-3 (95% highest probability density- HPD Interval: 1.09 x10^-3 to 2.08x10^-3) and 2.14x10^-3 (95% HPD Interval: 1.35 x10^-3 to 2.91x10^-3) per site per year, respectively, which is relatively low compared to structural proteins. The median times of the most recent common ancestors (tMRCA) were estimated to be around 1933 (95% HPD, 1907–1952) and 1956 (95% HPD, 1934–1970) for subtypes B and C, respectively. Our analysis shows that subtype C appeared in the global population two decades after the introduction of subtype B. A Gaussian Markov random field (GMRF) skyride coalescent analysis demonstrates that the early expansion rate of subtype B was quite high, rapidly progressing during the 1960s and 1970s to the early 1990s, after which the rate increased up to the 2010s. In contrast, HIV-1 subtype C exhibited a relatively slow occurrence rate until the late 1980s when there was a sharp increase up to the end of 1990s; thereafter, the rate of occurrence gradually slowed. Our study highlights the importance of examining the internal/regulatory genes of HIV-1 to understand its complete evolutionary dynamics. The study results will therefore contribute to better understanding of HIV-1 evolution.

Multilayered HIV-1 gag-specific T-cell responses contribute to slow progression in HLA-A*30-B*13-C*06-positive patients

Objective:

The HLA-A^∗30-B^∗13-C^∗06 haplotype is reported to be associated with slow disease progression in the HIV-1-infected Northern Han Chinese population, but the mechanism remains unknown.

Design:

Gag-specific T-cell responses and gag sequencing were performed in nine B′ clade HIV-1-infected HLA-A^∗30-B^∗13-C^∗06-positive slow progressors to understand HLA-associated viral control.

Methods:

Interferon-γ ELISPOT assays were performed to determine the Gag-specific T-cell responses and cross-reactivity to variant peptides. Longitudinal HIV-1 gag sequencing was performed at the clonal level.

Results:

The overlapping peptides (OLP)-48: RQANFLGKIWPSHKGRPGNF (RL42 Gag_434-453); OLP-2: GQLDRWEKIRLRPGGKKKYR (RL42 Gag_11-30); OLP-15: VQNLQGQMVHQPISPRTLNA (RL42 Gag_135-154) and OLP-16: HQPISPRTLNAWVKVVEEKA (RL42 Gag_144-163) were dominant in HLA-A^∗30-B^∗13-C^∗06-positive patients. A new epitope [HQPISPRTL (Gag_144-152, HL9)] within OLP-15 and OLP-16 was identified. Results showed that strong cross-reactive responses to multiple immunodominant peptides were associated with better clinical outcomes. In addition, efficient cross-recognition of HL9 autologous variants developed in patients was associated with high CD4⁺ T-cell counts. However, two patients who had developed mutations to their dominant responses during the follow-up experienced decrease in CD4⁺ T-cell counts. It appears that Gag-specific T-cell responses against one or more unmutated epitopes or cross-recognition of autologous epitope variants contribute to slow disease progression in HLA-A^∗30-B^∗13-C^∗06-positive patients.

Conclusion:

We conclude that a single ‘appropriate’ Gag-specific T-cell response appears to be sufficient to protect patients from disease progression. HLA-A^∗30-B^∗13-C^∗06-positive individuals benefited from having a choice of numerous immunodominant gag epitopes for T cells to react. The study offers new insight for future design of T-cell-based HIV-1 vaccine.

Cross-border sexual transmission of the newly emerging HIV-1 clade CRF51_01B

A novel HIV-1 recombinant clade (CRF51_01B) was recently identified among men who have sex with men (MSM) in Singapore. As cases of sexually transmitted HIV-1 infection increase concurrently in two socioeconomically intimate countries such as Malaysia and Singapore, cross transmission of HIV-1 between said countries is highly probable. In order to investigate the timeline for the emergence of HIV-1 CRF51_01B in Singapore and its possible introduction into Malaysia, 595 HIV-positive subjects recruited in Kuala Lumpur from 2008 to 2012 were screened. Phylogenetic relationship of 485 amplified polymerase gene sequences was determined through neighbour-joining method. Next, near-full length sequences were amplified for genomic sequences inferred to be CRF51_01B and subjected to further analysis implemented through Bayesian Markov chain Monte Carlo (MCMC) sampling and maximum likelihood methods. Based on the near full length genomes, two isolates formed a phylogenetic cluster with CRF51_01B sequences of Singapore origin, sharing identical recombination structure. Spatial and temporal information from Bayesian MCMC coalescent and maximum likelihood analysis of the protease, gp120 and gp41 genes suggest that Singapore is probably the country of origin of CRF51_01B (as early as in the mid-1990s) and featured a Malaysian who acquired the infection through heterosexual contact as host for its ancestral lineages. CRF51_01B then spread rapidly among the MSM in Singapore and Malaysia. Although the importation of CRF51_01B from Singapore to Malaysia is supported by coalescence analysis, the narrow timeframe of the transmission event indicates a closely linked epidemic. Discrepancies in the estimated divergence times suggest that CRF51_01B may have arisen through multiple recombination events from more than one parental lineage. We report the cross transmission of a novel CRF51_01B lineage between countries that involved different sexual risk groups. Understanding the cross-border transmission of HIV-1 involving sexual networks is crucial for effective intervention strategies in the region.

Phylogenetic and temporal dynamics of human immunodeficiency virus type 1B in China: four types of B strains circulate in China

To investigate the origin and evolutionary history of the spread of HIV-1 subtype B in China, a total of 409 sequences of pol gene sampled from 1994 to 2012 in 29 provinces across China was subjected to phylogenetic and Bayesian molecular clock analyses. The study reveals that subtype B strains in China are genetically diverse and can be classified into four distinct subgroups, namely B' (Thai-B), BJ-B (Beijing-B), Pan-B (Pandemic-B), and TW-B (Taiwan-B), according to the origin of the sequences. The BJ-B and TW-B are reported for the first time. Phylogeographic analysis reveals that B' exhibits a nationwide, transprovincial distribution, and is found in 21 provinces in China in this study, whereas the Pan-B, BJ-B, and TW-B lineages are restricted to particular regions. From the same common ancestor of B', there arise two subclusters in which sequences from Yunnan occupy the basal position. The times of the most recent common ancestors (tMRCAs) of B' and BJ-B are estimated to be 1983.6 (1975.9-1990.3) and 1995.3 (1989.6-2000.3), respectively. The skyline plot profile reveals an exponential decrease in median number of effective infections of subtype B in China from 1994 to 2009. The existence of four types of B clades also indicates distinct transmission networks of subtype B, originating from different introduction events at different time points. The data presented here offer a new perspective on the epidemic of HIV-1 subtype B in China.

Selective whole genome amplification for resequencing target microbial species from complex natural samples

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with <6.7-fold amplification of the background. SWGA-treated genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs.

Differential selection in HIV-1 gp120 between subtype B and East Asian variant B'

HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world. For instance, distinct genomic backgrounds can be observed between the pandemic subtype B, prevalent in Europe and North-America, and its offspring clade B' in East Asia. Here we ask whether this differentiation affects the selection pressure experienced by the virus. To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio k a /k s of amino acid changes to synonymous changes. To validate the approach we compare results to those from a state-of-the-art mixed-effect method. The agreement is acceptable, but the analysis also demonstrates some limitations of the simpler approach. Further, we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B' with more directional selection pressure in variable loops and more stabilizing selection in the constant regions. Focusing on codons with increased k a /k s values in B', we show that these codons are scattered over the whole of gp120, with remarkable clusters of higher density in regions flanking the variable loops. We identify a significant statistical association of glycosylation sites and codons with increased k a /k s values.

Phylodynamic profile of HIV-1 subtype B, CRF01_AE and the recently emerging CRF51_01B among men who have sex with men (MSM) in Singapore

HIV-1 subtype B and CRF01_AE are the predominant infecting subtypes among men who have sex with men (MSM) in Singapore. The genetic history, population dynamics and pattern of transmission networks of these genotypes remain largely unknown. We delineated the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and the recently characterized CRF51_01B strains circulating among the MSM population in Singapore. A total of 105 (49.5%) newly-diagnosed treatment-naïve MSM were recruited between February 2008 and August 2009. Phylogenetic reconstructions of the protease gene (HXB2: 2239 – 2629), gp120 (HXB2: 6942 – 7577) and gp41 (HXB2: 7803 – 8276) of the env gene uncovered five monophyletic transmission networks (two each within subtype B and CRF01_AE and one within CRF51_01B lineages) of different sizes (involving 3 – 23 MSM subjects, supported by posterior probability measure of 1.0). Bayesian coalescent analysis estimated that the emergence and dissemination of multiple sub-epidemic networks occurred between 1995 and 2005, driven largely by subtype B and later followed by CRF01_AE. Exponential increase in effective population size for both subtype B and CRF01_AE occurred between 2002 to 2007 and 2005 to 2007, respectively. Genealogical estimates suggested that the novel CRF51_01B lineages were probably generated through series of recombination events involving CRF01_AE and multiple subtype B ancestors. Our study provides the first insight on the phylodynamic profiles of HIV-1 subtype B, CRF01_AE and CRF51_01B viral strains circulating among MSM in Singapore.

Evolutionary history of HIV-1 subtype B and CRF01_AE transmission clusters among men who have sex with men (MSM) in Kuala Lumpur, Malaysia

HIV-1 epidemics among men who have sex with men (MSM) continue to expand in developed and developing countries. Although HIV infection in MSM is amongst the highest of the key affected populations in many countries in Southeast Asia, comprehensive molecular epidemiological study of HIV-1 among MSM remains inadequate in the region including in Malaysia. Here, we reported the phylodynamic profiles of HIV-1 genotypes circulating among MSM population in Kuala Lumpur, Malaysia. A total of n = 459 newly-diagnosed treatment-naïve consenting subjects were recruited between March 2006 and August 2012, of whom 87 (18.9%) were self-reported MSM. Transmitted drug resistance mutations were absent in these isolates. Cumulatively, phylogenetic reconstructions of the pro-rt gene (HXB2∶2253-3275) showed that HIV-1 subtype B and CRF01_AE were predominant and contributed to approximately 80% of the total HIV-1 infection among MSM. In addition to numerous unique transmission lineages within these genotypes, twelve monophyletic transmission clusters of different sizes (2-7 MSM sequences, supported by posterior probability value of 1) were identified in Malaysia. Bayesian coalescent analysis estimated that the divergence times for these clusters were mainly dated between 1995 and 2005 with four major transmission clusters radiating at least 12 years ago suggesting that active spread of multiple sub-epidemic clusters occurred during this period. The changes in effective population size of subtype B showed an exponential growth within 5 years between 1988 and 1993, while CRF01_AE lineage exhibited similar expansion between 1993 and 2003. Our study provides the first insight of the phylodynamic profile of HIV-1 subtype B and CRF01_AE circulating among MSM population in Kuala Lumpur, Malaysia, unravelling the importance of understanding transmission behaviours as well as evolutionary history of HIV-1 in assessing the risk of outbreak or epidemic expansion.

A single early introduction of HIV-1 subtype B into Central America accounts for most current cases

Human immunodeficiency virus type 1 (HIV-1) variants show considerable geographical separation across the world, but there is limited information from Central America. We provide the first detailed investigation of the genetic diversity and molecular epidemiology of HIV-1 in six Central American countries. Phylogenetic analysis was performed on 625 HIV-1 pol gene sequences collected between 2002 and 2010 in Honduras, El Salvador, Nicaragua, Costa Rica, Panama, and Belize. Published sequences from neighboring countries (n = 57) and the rest of the world (n = 740) were included as controls. Maximum likelihood methods were used to explore phylogenetic relationships. Bayesian coalescence-based methods were used to time HIV-1 introductions. Nearly all (98.9%) Central American sequences were of subtype B. Phylogenetic analysis revealed that 437 (70%) sequences clustered within five significantly supported monophyletic clades formed essentially by Central American sequences. One clade contained 386 (62%) sequences from all six countries; the other four clades were smaller and more country specific, suggesting discrete subepidemics. The existence of one large well-supported Central American clade provides evidence that a single introduction of HIV-1 subtype B in Central America accounts for most current cases. An introduction during the early phase of the HIV-1 pandemic may explain its epidemiological success. Moreover, the smaller clades suggest a subsequent regional spread related to specific transmission networks within each country.

A small set of succinct signature patterns distinguishes Chinese and non-Chinese HIV-1 genomes

The epidemiology of HIV-1 in China has unique features that may have led to unique viral strains. We therefore tested the hypothesis that it is possible to find distinctive patterns in HIV-1 genomes sampled in China. Using a rule inference algorithm we could indeed extract from sequences of the third variable loop (V3) of HIV-1 gp120 a set of 14 signature patterns that with 89% accuracy distinguished Chinese from non-Chinese sequences. These patterns were found to be specific to HIV-1 subtype, i.e. sequences complying with pattern 1 were of subtype B, pattern 2 almost exclusively covered sequences of subtype 01_AE, etc. We then analyzed the first of these signature patterns in depth, namely that L and W at two V3 positions are specifically occurring in Chinese sequences of subtype B/B' (3% false positives). This pattern was found to be in agreement with the phylogeny of HIV-1 of subtype B inside and outside of China. We could neither reject nor convincingly confirm that the pattern is stabilized by immune escape. For further interpretation of the signature pattern we used the recently developed measure of Direct Information, and in this way discovered evidence for physical interactions between V2 and V3. We conclude by a discussion of limitations of signature patterns, and the applicability of the approach to other genomic regions and other countries.

Neutralization sensitivity of HIV-1 subtype B' clinical isolates from former plasma donors in China

BACKGROUND

HIV-1 subtype B' isolates have been predominantly circulating in China. Their intra- and inter-subtype neutralization sensitivity to autologous and heterologous plasmas has not been well studied.

RESULTS

Twelve HIV-1 B' clinical isolates obtained from patients were tested for their intra- and inter-subtype neutralization sensitivity to the neutralization antibodies in the plasmas from patients infected by HIV-1 B' and CRF07_BC subtypes, respectively. We found that the plasmas from the HIV-1 B'-infected patients could potently neutralize heterologous viruses of subtype B' with mean ID50 titer (1/x) of about 67, but they were not effective in neutralizing autologous viruses of subtype B' with mean ID50 titer (1/x) of about 8. The plasmas from HIV-1 CRF07_BC-infected patients exhibited weak inter-subtype neutralization activity against subtype B' viruses with ID50 titer (1/x) is about 22. The neutralization sensitivity of HIV-1 B' isolates was inversely correlated with the neutralizing activity of plasmas from HIV-1 B'-infected patients (Spearman's r = -0.657, P = 0.020), and with the number of potential N-glycosylation site (PNGS) in V1-V5 region (Spearman's r = -0.493, P = 0.034), but positively correlated with the viral load (Spearman's r = 0.629, P = 0.028). It had no correlation with the length of V1-V5 regions or the CD4+ T cell count. Virus AH259V has low intra-subtype neutralization sensitivity, it can be neutralized by 17b (IC50: 10μg/ml) and 447-52D (IC50: 1.6μg/ml), and the neutralizing antibodies (nAbs) in plasma AH259P are effective in neutralizing infection by the primary HIV-1 isolates with different subtypes with ID50 titers (1/x) in the range of 32-396.

CONCLUSIONS

These findings suggest that the HIV-1 subtype B' viruses may mutate under the immune pressure, thus becoming resistant to the autologous nAbs, possibly by changing the number of PNGS in the V1-V5 region of the viral gp120. Some of primary HIV-1 isolates are able to induce both intra- and inter-subtype cross-neutralizing antibody responses.

Screening for and verification of novel mutations associated with drug resistance in the HIV type 1 subtype B(') in China

OBJECTIVE

Mutations associated with HIV drug resistance have been extensively characterized at the HIV-1 polymerase domain, but more studies have verified that mutations outside of the polymerase domain also results in resistance to antiviral drugs. In this study, mutations were identified in 354 patients experiencing antiretroviral therapy (ART) failure and in 97 naïve-therapy patients. Mutations whose impact on antiviral drugs was unknown were verified by phenotypic testing.

METHODS

Pol sequences of HIV subtype B(') obtained from patients experiencing ART failure and from naïve-therapy patients were analyzed for mutations distinct between two groups. Mutations that occurred at a significantly higher frequency in the ART failure than the naïve-therapy group were submitted to the Stanford HIV Drug Resistance Database (SHDB) to analyze the correlation between HIV mutations and drug resistance. For mutations whose impact on the antiviral drug response is unknown, the site-directed mutagenesis approach was applied to construct plasmids containing the screened mutations. 50% inhibitory concentration (IC(50)) to AZT, EFV and NVP was measured to determine the response of the genetically constructed viruses to antiviral drugs.

RESULTS

7 mutations at 6 positions of the RT region, D123E, V292I, K366R, T369A, T369V, A371V and I375V, occurred more frequently in the ART failure group than the naïve-therapy group. Phenotypic characterization of these HIV mutants revealed that constructed viruses with mutations A371V and T369V exhibited dual resistance to AZT and EFV respectively, whereas the other 5 mutations showed weak resistance. Although the impact of the other six mutations on response to NVP was minimal, mutation T369V could enhance resistance to NVP.

CONCLUSIONS

This study demonstrated that mutations at the RT C-terminal in subtype B' could result in resistance to RT inhibitors if the mutations occurred alone, but that some mutations could promote susceptibility to antiviral drugs.

Phylodynamics of HIV-1 unique recombinant forms in China-Myanmar border: implication for HIV-1 transmission to Myanmar from Dehong, China

China-Myanmar border plays a crucial role in HIV-1 transmission in Asia. Here, we performed Bayesian phylodynamics analyses on p17 gene using BEAST to investigate HIV-1 transmission in this region. Maximum clade credibility trees of subtype C and CRF01_AE show that majority of unique recombinant forms (URFs) and pure subtype strains from Dehong and Myanmar cluster together, forming large clades with ancestral geographical states of Dehong. Bayes factor tests support the statistically significant geographic diffusion link between Dehong and Myanmar. The estimated time to the most recent common ancestor of Myanmar URFs_BC (1999.2) was later than that of Dehong URFs_BC (1998.0), but earlier than that of Myanmar URFs_01BC (2004.3). Since 1998, HIV-1 recombination between subtypes B, C and CRF01_AE has been continuously occurring in China-Myanmar border region. These results suggest that HIV-1 subtypes B, C and CRF01_AE were most likely transmitted from Dehong to Myanmar, and predict that URFs_01BC should be also prevalent in Dehong, Yunnan.

Estimating the origin and evolution characteristics for Korean HIV type 1 subtype B using Bayesian phylogenetic analysis

The majority of Korean human immunodeficiency virus type 1 (HIV-1) isolates are composed of the Korean clade B strain that is distinct from the subtype B prevalent in North America and Europe. However, it is still not clear how HIV-1 was introduced, transmitted, and evolved within the Korean population. To identify the evolutionary characteristics of Korean HIV-1, we estimate the molecular epidemic history of HIV-1 subtype B gp120 env in Korea in comparison with sequences isolated from other geographic locations. A Bayesian Markov chain Monte Carlo (MCMC) statistical inference was used to estimate the time of divergence of subtype B. The estimated time of divergence of subtype B and the distinct monophyletic Korean B cluster was estimated to be in the early and mid-1960s, respectively. Substitution rates were estimated at 7.3×10(-3) and 8.0×10(-3) substitutions per site per year for HIV-1 subtype B and Korean clade B, respectively. The demographic dynamics of two Korean data sets showed that the effective number of infections in Korea increased rapidly until the early 1980s, and then the rate only slowly increased until the mid-1990s when the population growth approached a steady-state. These results suggest that the growth rate of prevalent HIV-1 strains in Korea was lower than in other countries, suggesting that the evolution of HIV-1 Korean clade B was relatively slow. Furthermore, the limited transmission of HIV-1 within the Korean population likely led to the independent evolution of this virus to form the HIV-1 Korean clade B.

Tracing the origin and history of HIV-1 subtype B' epidemic by near full-length genome analyses

OBJECTIVE

To investigate the origin and evolutionary history of HIV-1 subtype B' responsible for the epidemic among injecting drug users (IDUs), former plasma donors (FPDs) and the subsequent heterosexual transmission in China.

METHODS

A total of 33 sequences of subtype B' near full-length genomes (NFLGs) sampled during 1998-2009 in 11 provinces across China were determined. The NFLGs were subjected to Bayesian molecular clock analyses to estimate the time of the most recent common ancestors (tMRCAs) and to reconstitute the time-space process of subtype B' dissemination in China.

RESULTS

The study revealed that subtype B' strains in China can be classified into two distinct subgroups: a monophyletic B' cluster (B'CN*) consisting of subtype B' sequences mainly from FPDs and heterosexuals across China outside of Yunnan; B' strains circulating among IDUs in Yunnan (B'YN) that occupy the most basal position of B' clade in China. The tMRCAs of B'YN and B'CN* were estimated to be 1985 (1982-1987) and 1989 (1987-1991), respectively. The skyline plot profile revealed the explosive nature of subtype B' expansion in central China in the mid-1990s.

CONCLUSION

Our results suggest that subtype B' epidemics among FPDs and heterosexuals in inland China were most likely originated from a single founding subtype B' strain that had been circulating among IDUs in Yunnan province. Yunnan province plays a pivotal role in bridging the preexisting subtype B' epidemics in south-east Asia with the subsequent epidemic among FPDs and heterosexuals in inland China.

Genetic diversity and molecular epidemiology of HIV transmission

The high genetic diversity of HIV is one of its most significant features, as it has consequences in global distribution, vaccine design, therapy success, disease progression, transmissibility and viral load testing. Studying HIV diversity helps to understand its origins, migration patterns, current distribution and transmission events. New advances in sequencing technologies based on the parallel acquisition of data are now used to characterize within-host and population processes in depth. Additionally, we have seen similar advances in statistical methods designed to model the past history of lineages (the phylodynamic framework) to ultimately gain better insights into the evolutionary history of HIV. We can, for example, estimate population size changes, lineage dispersion over geographic areas and epidemiological parameters solely from sequence data. In this article, we review some of the evolutionary approaches used to study transmission patterns and processes in HIV and the insights gained from such studies.

High prevalence of HIV type 1 subtype B' among heterosexuals in Western Hubei, Central China: bridging the epidemic into the general population

A molecular epidemiological investigation (n = 62) conducted in western Hubei, Central China, revealed that HIV-1 subtype B' (Thailand variant of subtype B) predominated not only among former plasma donors (FPDs) (29/29, 100%) but also among heterosexuals (27/31, 87%), suggesting that subtype B' appears to bridge the spread from FPDs in the general population in this particular area in Central China.

The non-random clustering of non-synonymous substitutions and its relationship to evolutionary rate

Background

Protein sequences are subject to a mosaic of constraint. Changes to functional domains and buried residues, for example, are more apt to disrupt protein structure and function than are changes to residues participating in loops or exposed to solvent. Regions of constraint on the tertiary structure of a protein often result in loose segmentation of its primary structure into stretches of slowly- and rapidly-evolving amino acids. This clustering can be exploited, and existing methods have done so by relying on local sequence conservation as a signature of selection to help identify functionally important regions within proteins. We invert this paradigm by leveraging the regional nature of protein structure and function to both illuminate and make use of genome-wide patterns of local sequence conservation.

Results

Our hypothesis is that the regional nature of structural and functional constraints will assert a positive autocorrelation on the evolutionary rates of neighboring sites, which, in a pairwise comparison of orthologous proteins, will manifest itself as the clustering of non-synonymous changes across the amino acid sequence. We introduce a dispersion ratio statistic to test this and related hypotheses. Using genome-wide interspecific comparisons of orthologous protein pairs, we reveal a strong log-linear relationship between the degree of clustering and the intensity of constraint. We further demonstrate how this relationship varies with the evolutionary distance between the species being compared. We provide some evidence that proteins with a history of positive selection deviate from genome-wide trends.

Conclusions

We find a significant association between the evolutionary rate of a protein and the degree to which non-synonymous changes cluster along its primary sequence. We show that clustering is a non-redundant predictor of evolutionary rate, and we speculate that conflicting signals of clustering and constraint may be indicative of a historical period of relaxed selection.

Viral phylodynamics and the search for an 'effective number of infections'

Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the ‘effective number of infections’, a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.

Explosive HIV-1 subtype B' epidemics in Asia driven by geographic and risk group founder events

We explored the timescale, spatial spread, and risk group population structure of HIV-1 subtype B', the cause of explosive blood-borne HIV-1 epidemics among injecting drug users (IDUs) and former plasma donors (FPDs) in Asia. Sequences from FPDs in China formed a distinct monophyletic cluster within subtype B'. Further analysis revealed that subtype B' was founded by a single lineage of pandemic subtype B around 1985. Subsequently, the FPD cluster appears to have derived from a single subtype B' lineage around 1991, corroborating the hypothesis that FPD outbreaks stemmed from the preceding epidemic among IDUs in Southeast Asia, most likely from the Golden-Triangle region.

Genetic and epidemiologic characterization of HIV-1 infection In Liaoning Province, China

BACKGROUND

Although many studies of HIV-1 in China have focused on high-risk injecting drug users and former blood donors in high prevalence regions, little is known about HIV-1 in relatively low prevalence provinces. Here, we compare the epidemiologic and genetic profile of HIV-1 in Liaoning-a low prevalence province-with those identified in China's most severely affected provinces.

MATERIALS AND METHODS

Two hundred eight HIV-1-positive subjects from all major cities in Liaoning province were recruited between 2000 and 2008. 2.6 kilobase gag-pol sequences were amplified from plasma viral RNA and sequenced directly. The HIV-1 sequences obtained were analyzed using phylogenetic and recombinant approaches.

RESULTS

We have shown that in recent years, although HIV-1 prevalence in Liaoning has remained low, the rate of new infection has increased rapidly, particularly among men who have sex with men and heterosexual risk individuals (together comprising >54% of infected individuals in 2007). Furthermore, phylogenetic analysis has identified all major subtypes/circulating recombinant forms of HIV-1 in Liaoning previously identified in high prevalence provinces. Our study also shows close relationships between HIV-1 subtype/circulating recombinant form and certain risk behaviors. Notably, men who have sex with men and heterosexual risk individuals harbor most divergent strains of HIV-1 from multiple high-risk groups.

CONCLUSIONS

Our study suggested that HIV-1 continues to spread to the general population through sexual contact; Liaoning, therefore, serves as the critical base for the introduction and spread of HIV-1 in northeast China. We believe the transmission patterns suggested herein will help guide public health workers in reducing further spread of HIV-1 within China.

Evolutionary analysis of the dynamics of viral infectious disease

Many organisms that cause infectious diseases, particularly RNA viruses, mutate so rapidly that their evolutionary and ecological behaviours are inextricably linked. Consequently, aspects of the transmission and epidemiology of these pathogens are imprinted on the genetic diversity of their genomes. Large-scale empirical analyses of the evolutionary dynamics of important pathogens are now feasible owing to the increasing availability of pathogen sequence data and the development of new computational and statistical methods of analysis. In this Review, we outline the questions that can be answered using viral evolutionary analysis across a wide range of biological scales.