Near full-length genome analysis of HIV type 1 CRF02.AG subtype C and CRF02.AG subtype G recombinants

Molecular Epidemiology of HIV-1 in African Countries: A Comprehensive Overview

The human immunodeficiency virus type 1 (HIV-1) originated in non-human primates in West-central Africa and continues to be a major global public health issue, having claimed almost 33 million lives so far. In Africa, it is estimated that more than 20 million people are living with HIV/Acquired Immunodeficiency Syndrome (AIDS) and that more than 730,000 new HIV-1 infections still occur each year, likely due to low access to testing. The high genetic variability of HIV-1, due to a fast replication cycle and high mutation rate, may cause the generation of many viral variants in a single infected patient during a single day. Therefore, the active monitoring and characterization of the HIV-1 subtypes and recombinant forms circulating through African countries poses a significant challenge to more specific diagnoses, treatments, care, and intervention strategies. In this review, a concise characterization of all the subtypes and recombinant forms circulating in Africa is presented to highlight the magnitude of the HIV-1 threat among the African countries and to understand virus genetic diversity and dispersion dynamics better.

HIV subtype diversity worldwide

PURPOSE OF REVIEW

To provide a summary of the current data on the global HIV subtype diversity and distribution by region. HIV is one of the most genetically diverse pathogens due to its high-mutation and recombination rates, large population size and rapid replication rate. This rapid evolutionary process has resulted in several HIV subtypes that are heterogeneously globally distributed.

RECENT FINDINGS

Subtype A remains the most prevalent strain in parts of East Africa, Russia and former Soviet Union countries; subtype B in Europe, Americas and Oceania; subtype C in Southern Africa and India; CRF01_AE in Asia and CRF02_AG in Western Africa. Recent studies based on near full-length genome sequencing highlighted the growing importance of recombinant variants and subtype C viruses.

SUMMARY

The dynamic change in HIV subtype distribution presents future challenges for diagnosis, treatment and vaccine design and development. An increase in recombinant viruses suggests that coinfection and superinfection by divergent HIV strains has become more common necessitating continuous surveillance to keep track of the viral diversity. Cheaper near full-length genome sequencing approaches are critical in improving HIV subtype estimations. However, missing subtype data and low sequence sampling levels are still a challenge in some geographical regions. VIDEO ABSTRACT: http://links.lww.com/COHA/A14.

The natural history of HIV-1 subtype E infection in young men in Thailand with up to 14 years of follow-up

OBJECTIVE

We evaluated the progression to AIDS and death among 228 men who seroconverted within a 6-month window when in the Royal Thai Army between 1991 and 1995.

DESIGN AND METHODS

Men (N = 228) who seroconverted to HIV at 21-23 years of age between 1991 and 1995 were evaluated up to 14 years after HIV seroconversion. The seroconverters were matched with men who were seronegative when they were discharged from the military. In 2005-2006, the vital status was determined through the national mortality database and survivors were contacted for follow-up clinical and immunological assessment. Death certificates, medical records and next of kin interviews were used to evaluate the causes of death.

RESULTS

As of March 2006, among 228 seroconverters, 56 (24.6%) were alive, 171 (75.0%) had died and one (0.4%) had undetermined status. Among 255 HIV-seronegative individuals at baseline, 15 (5.9%) had died. The median time from HIV seroconversion to death was 7.8 years. The median time to AIDS death was 8.4 years. The median times from seroconversion to clinical AIDS and a CD4 cell count less than 200 cells/mul were 7.2 years and 6.5 years, respectively. The median time from seroconversion to World Health Organization criteria for antiretroviral therapy was 6.3 years.

CONCLUSION

Our data indicate a more rapid progression to AIDS and death after HIV-1 infection among young Thai men than has been reported in similar aged men who were HAART-naive in western high income countries.

HIV-1 co-infection, superinfection and recombination

As the human immunodeficiency virus (HIV) pandemic progresses, an increasing number of recombinant viruses have been identified and in many geographical regions they are now the predominating strain. These recombinants are formed when an individual has acquired a co-infection or superinfection with more than one HIV-1 strain or subtype. Thus, dually infected individuals provide opportunities for studying HIV recombinants and viral interactions between infecting strains in vivo. The possible epidemiological, clinical and therapeutic implications of dual infections and recombination are many. Recombination may result in the emergence of more pathogenic and virulent HIV strains with altered fitness, tropism, and resistance to multiple drugs, and may hamper the development of subtype-based vaccines. This review is aimed at providing a more thorough understanding of dual infections (both co-infection and super-infection) and the possible consequences of the emergence of recombinant HIV-1 strains.

HIV‐1 Proteases from Drug‐Naive West African Patients Are Differentially Less Susceptible to Protease Inhibitors

BACKGROUND

Now that highly active antiretroviral therapy (HAART) is being initiated on a large scale in West Africa, it remains controversial whether protease inhibitors (PIs), originally designed and tested against human immunodeficiency virus type 1 (HIV-1) subtype B, are equally effective against the non-B subtypes that are prevalent in West African countries. In this study, we investigated whether Ghanaian HIV-1 isolates, as representatives of West African isolates, are susceptible to PIs.

METHODS

We first generated an HIV-1 protease cassette vector proviral DNA carrying a luciferase gene, which allows patient-derived HIV-1 proteases to be inserted and to be subjected to both genotypic and phenotypic assays. HIV-1 protease genes derived from 39 treatment-naive Ghanaian patients were used in this experiment as representatives of West African strains. The cloned patient-derived HIV-1 protease genes were first sequenced and then genetically compared. Phenotypic analysis was performed with Ghanaian HIV-1 protease-chimeric viruses in the presence of 6 different PIs. Structural models of HIV-1 protease homodimers were constructed by the molecular modeling software.

RESULTS

Genetic analysis of cloned patient-derived HIV-1 protease genes indicated that most of the Ghanaian HIV-1 proteases are placed as subtype CRF02_AG strains, which are phylogenetically distant from subtype B strains, and that Ghanaian HIV-1 proteases do not harbor known major mutations influencing drug resistance but commonly carry 2-3 minor mutations. Phenotypic analysis performed with HIV-1 protease-recombinant viruses in the presence of 6 different PIs revealed that Ghanaian HIV-1 proteases are differentially less susceptible to the PIs. In support of this finding of differential susceptibility, structural analysis showed a significant distortion of nelfinavir, but not of amprenavir, in the Ghanaian protease pocket, suggesting nelfinavir might be less insertable into the Ghanaian protease than into the protease of subtype B.

CONCLUSIONS

These findings provide implications for the combination of PIs during the introduction of HAART into West Africa.

Development and application of a high-throughput HIV type 1 genotyping assay to identify CRF02_AG in West/West Central Africa

In West/West Central Africa, CRF02_AG is the most prevalent HIV-1 strain and circulates in the milieu of rare subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs). The molecular complexity of HIV-1 epidemics in this region and the need to extensively sample large populations, such as in the case of vaccine trials, pose seemingly conflicting requirements between full-genome sequencing and high-throughput low-resolution assays. Here we describe the development and evaluation of a multiregion hybridization assay (MHAcrf02) for the efficient genotyping of CRF02_AG in West/West Central Africa. Subtype A, G, and CRF02_AG-specific fluorescent probes were designed flanking five recombination breakpoints in CRF02_AG and were used in real-time PCRs. A panel representing West/West Central African HIV-1 genetic diversity was evaluated by MHAcrf02. The sample set, previously characterized by full-genome sequencing, included CRF02_AG and CRF02_AG-containing recombinants (n = 28), other subtypes, CRFs, and URFs (n = 34). DNA from peripheral blood mononuclear cells, cocultures, and plasmids was used as template. When the patterns of probe reactivity were evaluated. CRF02_AG was identified with a 100% specificity and sensitivity. In conclusion, MHAcrf02 will permit more efficient characterization of HIV-1 in West/West Central Africa, where CRF02_AG is an important strain. Together with other regional genotyping assays MHAcrf02 will contribute to the development of a global picture of HIV-1 diversity and geographic distribution, providing a strong foundation for intervention, including vaccine development.

Molecular epidemiology of HIV in Ghana: Dominance of CRF02_AG

Recent studies showed the importance of CRF02_AG in West Africa, although the clinical relevance of these recombinant forms of HIV remains unknown. The present study aimed at determining the molecular diversity of HIV in Ghana and investigating the possible epidemiologic advantage of recombinant HIV-1. Plasma samples collected in 1999-2002 from two populations of HIV infected individuals (144 asymptomatic candidate blood donors and 169 AIDS patients) were studied and 249 of them were molecularly characterised in gag, pol, and env regions. Five molecular groups were identified: strains clustering with CRF02_AG in all regions (147/249 or 59%), recombinant strains clustering with CRF02_AG in one or two regions (50/249 or 20%), other subtypes, pure or recombinant, but not involving CRF02_AG (37/249 or 15%), HIV-2 (11/249 or 4.5%), and double infections (4/249 or 1.5%). There was no significant difference in the distribution of HIV-1 recombinant strains according to clinical presentation. No evidence of a significant increase in CRF02_AG prevalence between 1999 and 2002 was found. Irrespective of clinical condition, CRF02_AG is the predominant molecular form of HIV-1 in Kumasi, Ghana.

High genetic diversity of HIV-1 strains in Chad, West Central Africa

The genetic diversity of HIV-1 strains in Chad was documented with a total of 107 samples from patients attending the general hospital in N'Djamena, the capital city of Chad. The genetic subtypes were identified in the V3-V5 env and p24 gag regions by sequence and phylogenetic tree analyses. Of the 107 strains, 78 had the same subtype/CRF designation between env and gag. Four subtypes and three CRFs were found to cocirculate: subtype A, 20.5%; subtype D, 18.7%; CRF02_AG, 13.1%; CRF11_cpx, 13.1%; subtype G, 3.7%; CRF01_AE, 2.8%; and subtype F1, 0.9%. The remaining 29 strains (27%) had discordant subtypes or CRF designations between env and gag; in 15 of these 29 strains, a CRF was involved in the recombination event, and 10 were subtype G in gag and subtype A in env, forming a separate subcluster within subtypes G and A. Subtype D strains represent almost 20% of the HIV-1 strains circulating in Chad and form a separate subcluster in gag and env. Nearly full-length genome sequencing for two such strains (99TCD-MN011 and 99TCD-MN012) revealed that they represent nonrecombinant subtype D variants. Compared with neighboring countries, the genetic subtype distribution of HIV-1 strains in Chad is unique for several reasons: lower prevalence of CRF02, high prevalence of CRF11 and subtype D, and absence of CRF06. These data clearly show that subtype distribution is very heterogeneous in Africa, probably the result of different founder effects.

Full-length genome analysis of HIV-1 subtype C utilizing CXCR4 and intersubtype recombinants isolated in South Africa

The HIV-1 epidemic in South Africa is largely due to subtype C viruses, which preferentially use CCR5 as a coreceptor for infection. We describe full-length genome sequences of two CXCR4-utilizing HIV-1 subtype C viruses and two intersubtype recombinants from South Africa. Three of the viruses (99ZACM4, 99ZACM9, and 99ZASW7) were isolated in 1999 from AIDS patients in Johannesburg, and a fourth virus (98ZADu178) was isolated in Durban in 1998 from an asymptomatic female sex worker. Isolates 99ZASW7 and 99ZACM9 from Johannesburg were subtype C throughout the genome, 99ZASW7 used the CXCR4 coreceptor, and 99ZACM9 used both CCR5 and CXCR4. Isolate 98ZADu178 from Durban was a novel recombinant between subsubtype A2 and subtype C. The third isolate from Johannesburg, 99ZACM4, was a complex, novel recombinant with multiple breakpoints and contained segments of subtypes A, C, D, G, and K. These results establish the presence of intersubtype recombinants in South Africa, indicating that ongoing surveillance for other subtypes and recombinants is necessary.

Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon

Recombination is an efficient mechanism of HIV-1 to generate genetic variability. Some of the recombinant forms of HIV-1 that have been described are of epidemic importance, and they are referred to as circulating recombinant forms (CRFs). In this study, we characterized four HIV-1 isolates from Cameroon that had previously been classified as subtype J in the protease gene and as subtype A in the env C2-V5 region. Analyses of the nearly complete genomes revealed that two of the samples (95CM-1816 and 96CM-4496) had the same recombinant structure as CRF11-cpx. The two remaining samples (96CM-1849 and 96CM-4164) constituted a new recombinant virus variant with genomic regions identified as subtypes A, G, J, and CRF01-AE. This mosaic virus structure was found in two individuals who had no direct epidemiological relationship, and may thus represent a new CRF. The fragments that were classified as subtype J in the new recombinant form were more related to subtype J regions of the CRF11-cpx sequences than to the reference strains of subtype J. The complex structures of CRF11-cpx and our new recombinant form, which are both the result of at least four recombination events, exemplify the coming difficulties in characterizing the internal relationships and origins of future recombinant HIV-1 strains. The new recombinant structure has been designated CRF13-cpx in the Los Alamos HIV Sequence Database.

High prevalence of HIV-1 subtype G and natural polymorphisms at the protease gene among HIV-infected immigrants in Madrid

OBJECTIVES

Genetic characterization of HIV-1 subtypes among immigrants and natives infected overseas.

METHODS

Phylogenetic analysis of HIV-1 protease sequences obtained from 109 foreigners (mainly Africans) and 32 native individuals infected overseas attending a reference HIV/AIDS centre located in Madrid, Spain.

RESULTS

The overall rate of infection with HIV-1 non-B subtypes was 50.3% (71/141). Whereas 94.3% (67/71) belonged to immigrants (mostly Africans, 60/67), only 5.6% (4/71) were from native individuals (P < 0.05). The distribution of non-B subtypes was: 49 G, eight C, six A, four D, two F and two H. The high prevalence of subtype G was mainly related to individuals from west-central Africa. Interestingly, substitutions at three or more positions associated with protease inhibitor (PI) resistance were recognized in 52.6% of naive subjects carrying non-B subtypes, but only in 8% of those infected with B viruses (P < 0.05). The genotypes most frequently recognized among non-B and B subtypes occurred, respectively, at positions 36 (100 versus 12%), 20 (77.2 versus 0%), 63 (40.3 versus 64%), 82 (17.5 versus 0%), 10 (14 versus 12%), 77 (3.5 versus 34%), and 71 (0 versus 2%). Accordingly, changes I-36 and I-20 may be considered specific genetic markers for non-B, group M variants and subtype G infections, respectively.

CONCLUSION

Nearly two-thirds of foreigners with HIV-1 infection in Madrid carry non-B subtypes, subtype G (protease) being the most common among west-central African immigrants. The high rate of natural polymorphisms at the protease gene in non-B viruses may compromise the response to PI. Therefore, HIV subtyping should be considered in treatment guidelines.

Diversity of mosaic structures and common ancestry of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Argentina revealed by analysis of near full-length genome sequences

The findings that BF intersubtype recombinant human immunodeficiency type 1 viruses (HIV-1) with coincident breakpoints in pol are circulating widely in Argentina and that non-recombinant F subtype viruses have failed to be detected in this country were reported recently. To analyse the mosaic structures of these viruses and to determine their phylogenetic relationship, near full-length proviral genomes of eight of these recombinant viruses were amplified by PCR and sequenced. Intersubtype breakpoints were analysed by bootscanning and examining the signature nucleotides. Phylogenetic relationships were determined with neighbour-joining trees. Five viruses, each with predominantly subtype F genomes, exhibited mosaic structures that were highly similar. Two intersubtype breakpoints were shared by all viruses and seven by the majority. Of the consensus breakpoints, all nine were present in two viruses, which exhibited identical recombinant structures, and four to eight breakpoints were present in the remaining viruses. Phylogenetic analysis of partial sequences supported both a common ancestry, at least in part of their genomes, for all recombinant viruses and the phylogenetic relationship of F subtype segments with F subtype viruses from Brazil. A common ancestry of the recombinants was supported also by the presence of shared signature amino acids and nucleotides, either unreported or highly unusual in F and B subtype viruses. These results indicate that HIV-1 BF recombinant viruses with diverse mosaic structures, including a circulating recombinant form (which are widespread in Argentina) derive from a common recombinant ancestor and that F subtype segments of these recombinants are related phylogenetically to the F subtype viruses from Brazil.

The AG recombinant IbNG and novel strains of group M HIV-1 are common in Cameroon

The genetic diversity of group M HIV-1 is highest in west central Africa. Blood samples from four locations in Cameroon were collected to determine the molecular epidemiology of HIV-1. The C2-V5 region of envelope was sequenced from 39 of the 40 samples collected, and 7 samples were sequenced across the genome. All strains belonged to group M of HIV-1. The circulating recombinant form CRF02 AG (IbNG) was the most common strain (22/39, 56%). Two of these were confirmed by full genome analysis. Four samples (4/39, 10%) clustered with the sub-subtype F2 and one of these was confirmed by full genome sequencing. Recombinant forms, each different but containing subtype A, accounted for the next most common form (7/39, 18%). Among these recombinants, those combining subtypes A and G were the most common (4/7, 57%). Also found were 3 subtype A, 2 subtype G, and 1 subtype B strain. Many recombination break points were shared between IbNG and the other AG recombinants, though none of these other AG recombinants included IbNG as a parent. This suggests that there was an ancestral AG recombinant that gave rise to CRF02 AG (IbNG), the successful circulating recombinant form, and to others that were less successful and are now rare.