Abstract: Background: In Ghana, the HIV-1 profile has been quite dynamic. Previous reports identified HIV-1subtypes A, D and G present and recently the CRF02_AG has been described as the predominant molecular form of HIV-1 in Kumasi, Ghana. This underscores the need for constant molecular characterization of HIV-1 species in the country. Objective: To provide current updates on the nature of HIVsubtypes in Ghana, there is need for a user-friendly tool for routine monitoring of subtypes in the absence of cost-intensive and skill-demanding sequencing techniques. This work demonstrates the use of heteroduplex mobility assay (HMA) for rapid subtype detection of HIV-1 isolated from Ghanaian patients. Method: Viruses from 15 antibody-positive HIV-1 patients were isolated directly by co-culturing peripheral blood mononuclear cells (PBMC) with phytohemagglutinin (PHA)-stimulated donor PBMCs from an HIV seronegative individual and through HeLa cells positive for CD4/CXCR4/CCR5 (MAGIC-5A cells). That was followed by proviral DNA extraction. Heteroduplex Mobility Assay (HMA) technique was then performed on the HIV gag gene. Results: Using the HMA technique, newly isolated HIV-1 strains were subtyped as follows: There were seven subtype A (47%), two subtype G (13%) and six (40%) A/G recombinants. Conclusion: The HIV-1 CRF02_AG in Ghana has spread much more rapidly than the previously predominant subtype A over the years. Constant molecular characterization of HIV strains is necessary to enable clear elucidation of the prevailing HIV species in Ghana. This study presents the HMA as a useful tool for monitoring subtype emergence and distribution in the country.
The global epidemiology of HIV-1subtypes is very heterogeneous and varies greatly worldwide, even within regions of the same continent [11, 12]. During 2004–2007, subtype C accounted for nearly half (48%) of all global infections [4, 13]. It is considered endemic in sub-Saharan and Eastern Africa (where over two-thirds of infected individuals reside) followed by the Indian Pacific and southern region of Brazil. HIV-1 subtype A1 is more prevalent in Central Africa, Iran, Eastern Europe and Central Asia, as it accounts for 12% of the total sub- types. Subtypes A2 and A3 are found primarily in Africa. Subtype B is the most disseminated variant. It accounts for 11% and found mainly in the European Union, USA, Australia, North Africa and Japan [14, 15]. CRF02_AG accounts for 8% and CRF01_AE for 5%, and they occur mainly in Western Africa and Southeast Asia [2, 16]. Other CRFs and URFs are responsible for 4% of global infections, bringing the combined total of worldwide CRFs to 16% and all recombinants (CRFs plus URFs) to 20% . Other subtypes, such as subtype G and D, account for 5 and 2%, respectively, while subtypes F, H, J and K together cause fewer than 1% of HIV infections worldwide [18, 19].
Despite all this interest on HIV genetic diversity in this country, most studies have been conducted in urban and central parts of Cameroon (2, 10, 11). Studies involving other parts of the country like the NWR have not been adequately evaluated. The few studies undertaken in this region, even though sample sizes have been small (< 30 samples), have revealed a number of new strains [5, 12]. Due to the preexisting diverse HIV-1subtypes, there is a likelihood of increasing mixed infections that could lead to the development of diverse circulating recombinant forms. Based on this trend, there is a need for surveil- lance of these diverse HIVsubtypes, CRFs, and URFs that have implications on vaccine design and transmis- sion fitness in this region. This study was therefore con- ducted to ascertain the current circulating HIVsubtypes, CRFs, or URFs in the Northwest region of Cameroon.
Latency reactivation of 11 distinct HIV-1 subtype and re- combinant isolates. Although recent investigations examined the potential reactivation of latent reservoirs using pharmaco- logical agents, these focused exclusively on isolates from sub- type B—the subtype most prevalent in the United States and Europe (8, 14, 45, 49). However, due to significant sequence diversity in the LTRs of HIV-1subtypes (28, 56, 73), non- subtype B isolates may respond distinctly to these agents. In particular, subtypes with variable B and Sp1 elements may exhibit resistance to drugs, similar to the phenotypes observed for mutIII Sp1 and mutI NF- B versions of LGIT (Fig. 2A and B) (see Fig. S3 and S4 in the supplemental material). To examine strategies of latency reactivation for various HIV sub- types and to identify potential limitations for divergent pro- moters, we generated LGIT variants containing U3 regions specific to the following subtypes and recombinants: A, A2, A/G, B, B/C, B/F, D, F, H, and two distinct isolates of C (see Table S2 and Fig. S6 in the supplemental material). As this investigation focuses on the role of the cis-acting elements in reactivation from latency, model LGIT variants were con- structed with the U3 regions of each subtype or circulating recombinant forms (CRF) (Fig. 1B), but with the R (including TAR), U5, and Tat regions of subtype B. In addition to having diversity throughout the Sp1 and B sites, these various U3 enhancer regions also differ in other cis-regulatory elements, including AP-1, YY1, NFAT, COUP-TF, and ILF sites (Fig. 1B). The use of 11 subtype enhancer sequences representing HIV-1 isolates from five continents may help elucidate whether certain subtypes and CRFs would require drug regi-
Figure 2 Prevalence of Gag amino acid variants reported in patients failing PI-based therapies and their mapping to HIV-1 protein structures. (A) Prevalence of amino acid variations at 55 Gag positions in 8 HIV-1subtypes (A1, B, C, D, F1, G, 01_AE and 02_AG) given the Los Alamos full-length Gag sequence dataset (Table 2). Only Gag positions where amino acid substitutions have been observed during PI-based treatment are shown. For each position, the HXB2 index is shown at the top, followed by the most prevalent amino acids (bold) and amino acid variations in our sequence datasets. Amino acids with blue superscripts have prevalence above 10% and other amino acids have orange superscripts. (B) Structural representation of Gag polyprotein and mapping of the 13 PI-associated Gag substitutions identified in Table 3. The annotation of Gag polyproteins is shown at the top. Individual Gag protein structures are shown at the bottom. Gag substitutions are annotated and colored accordingly. Red surfaces indicate PI-associated Gag substitutions at the Gag C-terminal domain; other substitutions are shown in green. PDB data of Gag protein structures: matrix, 1HIW; capsid, 3NTE; p2, 1U57; nucleocapsid, 2M3Z; p6, 2C55. Visualization software: PyMOL V1.5 (http://www.pymol.org/).
In order to characterize the antiviral activity of human TRIM5 α in more detail human derived indicator cell lines over expressing wild type human TRIM5 α were generated and challenged with HIV-1 and HIV-2 viruses pseudotyped with HIV envelope proteins in comparison to VSV-G pseudotyped particles. HIV envelope protein pseudotyped particles (HIV-1[NL4.3], HIV-1[BaL]) showed a similar restriction to infection (12 fold inhibition) compared to VSV-G pseudotyped viruses after challenging TZM-huTRIM5 α cells. For HIV-2 a stronger restriction to infection was observed when the homologous envelope protein Env42S was pseudotyped onto these particles compared to VSV-G pseudotyped HIV-2 particles (8.6 fold inhibition versus 3.4 fold inhibition). It has been shown that HIV-2 is restricted by the restriction factor Lv2, acting on capsid like TRIM5 α . A mutation of amino acid 73 (I73V) of HIV-2 capsid renders this virus Lv2-insensitive. Lv2- insensitive VSV-G pseudotyped HIV-2/I73V particles showed a similar restriction to infection as did HIV-2[VSV-G] particles (4 fold inhibition). HIV-2 envelope protein (Env42S)-pseudotyped HIV-2/ I73V particles revealed a 9.3 fold increase in infection in TZM cells but remained restricted in TZM- huTRIM5 α cells (80.6 fold inhibition) clearly indicating that at least two restriction factors, TRIM5 α and Lv2, act on incoming HIV-2 particles. Further challenge experiments using primary isolates from different HIV-1subtypes and from HIV-1 group O showed that wild type human TRIM5 α restricted infection independent of coreceptor use of the infecting particle but to variable degrees (between 1.2 and 19.6 fold restriction).
Each dataset was a collection of sequenced HIV-1 ge- nomes. Each sequence consisted of a list of amino acids. In order to properly analyze these sequences, we con- verted each into a binary vector. Because there are twenty different possible amino acids, we mapped each amino acid to a unique twenty-dimensional binary vector. For example, we mapped the amino acid Alanine to the point [1, 0, 0, 0, 0...], while we mapped Arginine to [0, 1, 0, 0, 0...]. After all the amino acids in a sequence were converted, we concatenated these individual vectors into
The identification of newly acquired human immunodefi- ciency virus type 1 (HIV-1) infection provides important in- formation on the dynamics of the epidemic, transmission net- works, and patterns of transmitted drug resistance, guides public health intervention programs, and identifies candidates for clinical trials and vaccine strategies targeting early infec- tion. The serologic testing algorithm for recent HIV serocon- version (STARHS) assay, or detuned assay, differentiates between recent and established HIV infection by using a high- sensitivity/low-sensitivity dual enzyme immunoassay (EIA) (11). The method was first introduced in 1998 and has been applied successfully to epidemiological studies of newly diag- nosed HIV-1 infections worldwide (13, 16, 22). However, the assay suffers from a number of recognized limitations. Firstly, its availability is limited to a few centers worldwide. In addi- tion, the assay employs an indirect first-generation EIA that requires exacting laboratory conditions, rigorous standardiza- tion, and quality assurance procedures for its reliable and re- producible use (9, 16). An additional consideration is that discontinuation or modification of the basic platform assay may adversely affect the STARHS application.
Performance of the ViroSeq HIV-1 genotyping system. The ViroSeq HIV-1 genotyping system generated sufficient ampli- con for all subtypes tested and delivered sequence data on all of the panel members. Problems were encountered in the clar- ity of DNA sequence data produced on the model 377 DNA sequencer, where gels had to be repeated due to poor gel resolution. Approximately 50% of the panel members exhib- ited high background fluorescence in profiles generated on the model 377 DNA sequencer. Four of the subtypes other than HIV-1 subtype B (ZAM18, ETH2220, CM240, and BCP- KITA) and one B subtype (US4) had significant lengths of single-strand sequence due to the poor performance of one or two sequencing primers. Due to the clarity problems observed in the sequence data obtained from the model 377 DNA sequencer, 15 panel members were selected for retesting using the HIV-1 viral stocks with 5,000 RNA copies/ml. DNA se- quencing reaction products for these 15 specimens were frac- tionated by capillary electrophoresis. Sequencing profiles gen- erated using the model 3100 genetic analyzer showed well- defined peaks with little to no background fluorescence. All RT-PCR products generated using the ViroSeq RT-PCR mod- ule showed a single band amplicon of ⬃1,800 bp. Background contributed by nonspecific amplification as observed for the 1.0 RT-PCR primers used in the TRUGENE kit was not observed when purified amplicons from the ViroSeq test were fraction- ated through 1.2% agarose gels (Fig. 3). Amplification yields were excellent and in most cases exceeded the amount of amplified product generated in the TRUGENE assay. All HIV-1subtypes produced at least 18 ng of amplicon in 5 l of
In this study, HIV-1subtypes that were closely related were also identified. Similar cluster phenomenon has been observed in previous studies carried out elsewhere (Smith et al., 2009; Weng et al., 2014; Parczewski et al., 2015; Patino-Galindo et al., 2017). These clusters suggested that these patients might have been infected recently with the HIV-1 virus. It is worth noting that Cameroon, as well as other countries, is currently implementing the test and treat policy where all patients tested positive for HIV are placed on treatment irrespective of their CD4 + T cells count or WHO clinical stage. However, it could also be possible that the transmission of related viral sequences may correlate with shared social or risk-behaviour patterns such as scarification, intravenous drug use or HIV transmission between men having sex with men among others (Weng et al., 2014; Parczewski et al., 2015; Patino-Galindo et al., 2017). Several studies have shown that resistance mutations with minimal impact on viral fitness may be transmitted serially (Weng et al., 2014; Steegen et al., 2016). While having clinical implications, the potential benefit in identifying these clusters in public health requires further investigation to ascertain this fact. This will alleviate ongoing transmission originating from recently infected individuals or tracing back the potential index case (Smith et al., 2009; Weng et al., 2014). Identifying HIV clusters are important in helping public health officials to identify areas where interventions might be useful in preventing further spread of the infection. Thus, the presence of clustering is an important contribution to the spread of the resistant virus and requires further investigation with a wider population.
Accurate and sensitive quantification of human immunodeficiency virus type 1 (HIV-1) RNA has been invaluable as a marker for disease prognosis and for clinical monitoring of HIV-1 disease. The first generation of commercially available HIV-1 RNA tests were optimized to detect the predominant HIV-1 subtype found in North America and Europe, subtype B. However, these tests are frequently suboptimal in detecting HIV-1 genetic forms or subtypes found in other parts of the world. The goal of the present study was to evaluate the performance of a new viral load assay with non-subtype B viruses. A transcription-mediated amplification method for detection and quantitation of diverse HIV-1subtypes, called the Gen-Probe HIV-1 viral load assay, is under development. In this study we examined the performance of the Gen-Probe HIV-1 viral load assay relative to that of the commonly used commercial HIV-1 RNA assays using a panel of primary isolates from Kenya. For comparison, we included several subtype B cloned viruses, and we quantified each virus using an in-house quantitative-competitive reverse transcriptase PCR (QC-RT-PCR) method and gag p24 antigen cap-
Combined antigen and antibody screening (fourth-generation) assays reduce the diagnostic window period between the time of human immunodeficiency virus (HIV) infection and laboratory diagnosis by 4 days, on average, in comparison to antibody-only (third generation) enzyme immunoassays (EIAs). The aim of the present study was to assess whether the new VIDAS HIV DUO Ultra (Biomérieux, Marcy-l’Etoile, France) showed an improved sensitivity and specificity in comparison to licensed fourth-generation assays. A total of 16 seroconversion panels, 15 cell culture supernatants infected with different HIV type 1 (HIV-1) subtypes, and 257 potentially cross-reactive serum samples were tested with VIDAS DUO HIV Ultra, Genscreen Plus HIV Ag-Ab, Enzygnost HIV Integral, Enzymun-Test HIV Combi, Genscreen HIV1/2, version 2 (third-generation EIA), and Genetic Systems HIV-1 Ag EIA (p24 antigen assay). VIDAS HIV DUO Ultra showed a comparable sensitivity to the single p24 antigen assay in seroconversion panels and a dilution series of virus lysates. The diagnostic window was reduced with VIDAS HIV DUO Ultra by 3.82 days, on average, in comparison with the fourth-generation assay with the lowest sensitivity of the antigen detection module. HIV-1 infection was detected 5.88 days earlier than with third-generation EIA. The mean time delay between reverse transcription- PCR and VIDAS HIV DUO Ultra was only 2.31 days. The specificity of fourth-generation assays after retesting ranged between 98.1 and 100%. In conclusion, VIDAS HIV DUO Ultra can replace single-antigen screening for laboratory diagnosis and screening of HIV infection in blood donors. There was no evidence for a second diagnostic window due to impaired sensitivity of the antibody detection module of all the fourth-generation EIAs evaluated in the present study. The specificity after initial and/or repeated testing of VIDAS HIV DUO Ultra was equivalent to that of a third-generation assay.
observation is consistent with both the original design of the test primers for hybridization with subtype B gag sequences and the relative degree of homology between gag sequences from subtypes B, C, and D compared with the degree of ho- mology between gag sequences from other HIV-1subtypes. HIV-1 MONITOR version 1.5 accurately quantified the con- centration of HIV-1 subtype A through G RNA. A similar conclusion was reached in a separate study with plasma sam- ples from 96 patients infected with HIV-1subtypes A through E and G and aliquots of the particle count-standardized iso- lates in this report (37). Although version 1.5 of the test also used lower-stringency amplification conditions than version 1.0 of the test, this modification alone was insufficient to impart performance equivalent to that of version 1.0 of the test with non-subtype B isolates in control experiments (data not shown). Compared with U.S. Food and Drug Administration- cleared version 1.0 of the HIV-1 MONITOR Test, version 1.5 of the test should provide clinicians more reliable viral load data because the test is substantially less influenced by viral subtype.
Nucleotide sequences were aligned using the Clustal X program  and three strategies were used to well characterize the HIV-1 sequences as pure subtype, CRF- like or URF using the pol alignment: i) a Neighbor- Joining (NJ) phylogenetic tree was first built under the Tamura-Nei substitution model in 1000 bootstrapped data sets, as implemented in MEGA program ; ii) all sequences were subsequently subjected to bootscanning with the Simplot software version 3.5.1 , using refer- ence sequences representative of HIV-1subtypes A1, B, C, and F1 available in Los Alamos database, http://www. hiv.lanl.gov/components/sequence/HIV/search/search.html). Bootstrap values supporting branching with reference sequences were determined in NJ trees constructed using the K2-parameter model , based on 100 re- samplings, with a 300 nt sliding window moving in steps
Current HIV-1 genotyping assays were developed using subtype B viruses prevalent in Western countries. It is not clear whether these assays are appropriate for use among African patients, who are likely to be infected with non-B subtypes. We evaluated the Bayer TRUGENE HIV-1 genotyping (TG) assay using prospectively collected samples from HIV-1-infected individuals who acquired infection in either sub-Saharan Africa or the West (Europe, North America, and Australia). Plasma samples from 208 individuals with an HIV-1 viral load of >1,000 copies/ml were tested using version 1 primers supplied with the TG assay. If these failed, an alternative primer set version 1.5 was used. Of the 208 individuals, the likely origin of infection was Africa (n ⴝ 104), Western (n ⴝ 87) and “Others” (i.e., all other geographic locations or origin not certain; n ⴝ 17). Among the three groups, the version 1 primers were successful in 85 (82%), 77 (89%), and 13 (76%) individuals, respectively (P ⴝ 0.1). Of the remaining 32 samples, 30 were successfully amplified by using the version 1.5 primers. HIV-1subtypes deduced from the reverse transcriptase sequences correlated with the likely origin of infection: Africa (28A, 3B, 33C, 13D, 6G, 4J, 2K, 5CRF01_AE, and 10CRF02_AG), Western (86B and 1K), and Others (1A and 16B). The success of the version 1 primers correlated with viral load (P < 0.014) and not with HIV-1subtypes. A protocol based on version 1 primers, followed by 1.5 primers, was successful in sequencing 99% of the samples in this cohort.
One of the main challenges for implementation of viral load assays in an era of increasing global mobility is ensuring accurate quantitation of all major HIV-1subtypes, groups, and recombi- nants. Previous studies on the performance of quantitative assays carried out on limited numbers of HIV-1subtypes showed signif- icant variability between viral load assays on different subtypes. Underquantitation of subtype A1 samples by the NucliSens v2.0 and RealTime assays, of subtype C by the RealTime assay, and of subtypes G and CRF02_AG by the NucliSens EasyQ v2.0 test was observed relative to the Xpert and Aptima assays, particularly for samples in the lower viremic range (35). Similarly, subtype CRF02_AG was underestimated by the NucliSens EasyQ v2.0 test (36), while the Aptima assay showed greater sensitivity than the CAP/CTM or RealTime assay on viral isolates and clinical samples but equivalent quantification on clinical samples and isolates be- longing to HIV groups M, N, O, and P (34). An additional concern is the ability to test low-volume specimens and alternative speci- men matrices. The Aptima assay product insert describes dilution (1:3) testing of low-volume specimens by use of Aptima specimen diluent (Hologic). Alternative sample types successfully run on the Panther system using the Aptima assay include cervicovaginal lavage fluid (33), serum (34), and dried blood spots (37).
Knowledge of immune mechanisms responsible for the cross-protection between highly divergent viruses such as human immunodeficiency virus type 1 (HIV-1) and HIV-2 may contribute to an understanding of whether virus variability may be overcome in the design of vaccine candidates which are broadly protective across the HIVsubtypes. We demonstrate that despite the significant difference in virus amino acid sequence, the majority of HIV-2-infected individuals with different HLA molecules possess a dominant cytotoxic T-cell response which is able to recognize HIV-1 Gag protein. Furthermore, HLA-B5801-positive subjects show broad cross-recognition of HIV-1subtypes since they mounted a T-cell response that tolerated extensive amino acid substitutions within HLA-B5801-restricted HIV-1 and HIV-2 epitopes. These results suggests that HLA-B5801- positive HIV-2-infected individuals have an enhanced ability to react with HIV-1 that could play a role in cross-protection.
Thus, at the time of this work, subtype A was formally divided into only two sub-subtypes A1 and A2 and two other sub-subtypes, A3 and A4, were also proposed but not formally retained in the Los Alamos National Lab- oratory nomenclature. A partially described A5 sub- subtype has also been previously described based on analysis of recombinant viruses but no prototype of this strain has been identified to date . In our analysis, A3 and A4 confirmed to have a degree of diversity com- patible with sub-subtypes definition. Interestingly, the Former Soviet Union (FSU) cluster, resulting from the introduction of HIV-1 subtype A in intravenous drug users population of the former Soviet Union countries in the 80s , also depicted a high degree of diversity compatible with sub-subtype and, thus, is proposed in this work as a separate sub-subtype called A6. Before the presentation of this part of the current study at the International AIDS Society conference 2017, A2, A3 and the FSU cluster were only identified as sub-subtype A1 by available subtyping tools. Since then, A3, A4 and A6 sub-subtypes have been formally implemented into the Los Alamos National Laboratory HIV data- base and allow a quick and more accurate description of the subtype A diversity. In this work we also added the description of the A7 sub-subtype that was not pre- viously described. We also enlarged the analysis to all other HIV-1subtypes and identified evidence of further diversification consistent with distinct sub-subtypes among the subtype D. Thus, 3 sub-subtypes are pro- posed for this latter subtype, called D1 to D3, allowing a better description of D diversity despite the existence of a few outsider sequences. Their classification may have to continue to evolve in the future depending of the potential acquisition of new sequences.
The HIV/AIDS epidemic is a major global public health crisis. Currently, an estimated 33 million people world- wide are living with HIV-1 infection. The majority of cases (67%) are in sub-Saharan Africa [1,2]. Evolution of HIV-1 has assumed multiple guises which differ in geographic distribution . Three groups of HIV-1 have developed across the globe: M (major), O (outlying) and N (new) . Majority of HIV-1subtypes responsible for the AIDS pandemic belong to group M and phylogenetic analysis has further classified them into 11 pure HIV-1subtypes [5,6] and 43 circulating recombinant forms (CRFs). In Kenya, reports of diverse HIV-1subtypes and recom- binants abound [8-10]. Subtype A1 and its recombinants are the most prevalent and responsible for majority of AIDS cases , their presence in other regions of the world not withstanding .
Subtypes or circulating recombinant forms (CRFs) were de- termined by constructing phylogenetic trees and performing recombination analyses using ClustalX 2.0 (10) and Simplot 3.5.1 (8), respectively. To determine whether the genetic di- versity of HIV-1 strains circulating in Cameroon can play a role in the performance of the ViroSeq assay, we estimated the performance of each of the assay’s sequencing primers accord- ing to viral subtypes in our sample panel. In addition, we estimated the binding position of these primers within the gag-pol region based on the position where the sequence gen- erated by the primer started. We did that because ViroSeq primers are not publicly accessible for such analyses. We there- fore studied the variability of sequences in these areas where the primers are expected to bind, using the online tool Seq- Publish from Los Alamos (http://www.hiv.lanl.gov) and HIV-1 subtype B HXB2 (accession no. K03455) as the reference se- quence in the alignment. Also, we included in the alignment a set of HIV-1subtypes B sequences from GenBank (http://www .hiv.lanl.gov) and the sequences from our sample panel.