Introduction Of Subtype Research Articles

In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography.

Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004–2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpret the epidemiological relevance of the drivers of spread we are able to identify. While the workflow we present here could be applied to other virus datasets of a similar scale, the characteristic star-like shape of HIV-1 phylogenies poses a serious obstacle to reconstructing a detailed evolutionary and spatial history for HIV-1 subtype B in the US.

Session types and subtyping for orchestrated interactions

In the setting of the π-calculus with binary sessions, we aim at relaxing the notion of duality of session types by the concept of retractable compliance developed in contract theory. This leads to extending session types with a new type operator of “speculative selection” including choices not necessarily offered by a compliant partner. We address the problem of selecting successful communicating branches by means of an operational semantics based on orchestrators, which has been shown to be equivalent to the retractable semantics of contracts, but clearly more feasible. A type system, sound with respect to such a semantics, is hence provided. The introduction of subtyping when interactions are orchestrated naturally leads to explicit subtyping, where coercions are functors on orchestrators. Besides, priority-governed selection policies (either at type- or process-level) are investigated in order to get rid of nondeterministic behaviours but those of the partner processes of the interactions.

A Population-Structured HIV Epidemic in Israel: Roles of Risk and Ethnicity.

BackgroundHIV in Israel started with a subtype-B epidemic among men who have sex with men, followed in the 1980s and 1990s by introductions of subtype C from Ethiopia (predominantly acquired by heterosexual transmission) and subtype A from the former Soviet Union (FSU, most often acquired by intravenous drug use). The epidemic matured over the last 15 years without additional large influx of exogenous infections. Between 2005 and 2013 the number of infected men who have sex with men (MSM) increased 2.9-fold, compared to 1.6-fold and 1.3-fold for intravenous drug users (IVDU) and Ethiopian-origin residents. Understanding contemporary spread is essential for effective public health planning.MethodsWe analyzed demographic and virologic data from 1,427 HIV-infected individuals diagnosed with HIV-I during 1998–2012. HIV phylogenies were reconstructed with maximum-likelihood and Bayesian methods.ResultsSubtype-B viruses, but not A or C, demonstrated a striking number of large clusters with common ancestors having posterior probability ≥0.95, including some suggesting presence of transmission networks. Transmitted drug resistance was highest in subtype B (13%). MSM represented a frequent risk factor in cross-ethnic transmission, demonstrated by the presence of Israeli-born with non-B virus infections and FSU immigrants with non-A subtypes.ConclusionsReconstructed phylogenetic trees demonstrated substantial grouping in subtype B, but not in non-MSM subtype-A or in subtype-C, reflecting differences in transmission dynamics linked to HIV transmission categories. Cross-ethnic spread occurred through multiple independent introductions, with MSM playing a prevalent role in the transmission of the virus. Such data provide a baseline to track epidemic trends and will be useful in informing and quantifying efforts to reduce HIV transmission.

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.

Tracing the origin and dynamics of the HIV-1 epidemic in Serbia

Since the first report of HIV infection in Serbia in 1985, the HIV-1 epidemic was very dynamic, changing the pattern in subtype distribution and prevailing transmission routes. To better understand the origin and epidemiological dynamics of HIV-1, we analyzed 266 (pol) sequences from Serbian patients diagnosed over a period of 14 years. Subtype distribution in Serbia is still marked by a prevailing subtype B genetic form. The transmission pattern, however, has changed from being intravenous drug user (IVDU) - driven to predominantly sexual transmission. The estimated time of initial founder strain introduction of sequences from Serbian IVDUs and MSM (men who have sex with men) is similar and dates back to the early 1980s, while introduction of subtype C occurred much more recently.

Molecular Dating of HIV-1 Subtype C from Bangladesh

Bangladesh has an overall low HIV prevalence of <0.1% in the general population and <1% among key affected populations, but it is one of few Asian countries that has yet to reverse the epidemic. In order to do this, it is important to understand the transmission dynamics in this country. The aim of this study was to investigate the phylogenetic relationships of HIV-1 subtype C strains from Bangladesh and related strains from other countries, and thereby clarify when and from where subtype C was introduced in the country and how it subsequently spread within Bangladesh. The phylogenetic analysis included 118 Bangladeshi gag sequences and 128 sequences from other countries and was performed using the BEAST package. Our analysis revealed that the vast majority of Bangladeshi sequences (97/118, 82%) fall into a large regional cluster of samples from Bangladesh, India, China and Myanmar, which dates back to the early 1960’s. Following its establishment in the region, this strain has entered Bangladesh multiple times from around 1975 and onwards, but extensive in-country transmission could only be detected among drug users and not through sexual transmission. In addition, there have been multiple (at least ten) introductions of subtype C to Bangladesh from outside this region, but no extensive spread could be detected for any of these. Since many HIV-infections remain undetected while asymptomatic, the true extent of the transmission of each strain remains unknown, especially among hard to reach groups such as clients of sex workers and returning migrants with families.

HIV Type 1 in Fiji Is Caused by Subtypes C and B

The HIV epidemic in Fiji remains largely uncharacterized. By February 2009, there were 294 confirmed cases; the majority occurred among the 20- to 39-year old age group and resulted from heterosexual contact. There are currently no published data concerning HIV subtypes in Fiji. In this study, venous blood samples were collected as dried blood spots from 35 HIV-positive individuals in Fiji. HIV-1 subtype was determined for 27 (77%) samples and the presence of four different subtypes, with multiple introductions of two, was demonstrated. Subtype distribution was as follows: 16 (59%) were subtype C, 9 (33%) were subtype B, 1 (4%) was subtype A, and 1 (4%) was subtype G. Phylogenetic analysis showed a clear segregation of the Fijian subtype C isolates and previously published Papua New Guinea subtype C isolates as well as multiple introductions of subtype B. These findings represent the first HIV-1 subtype data from the Fiji Islands.

Evolutionary Dynamics of HIV-1 BF and CB Recombinants and Its Parental Counterparts in South America

Analysis of the near full-length genomes revealed that the subtype F appeared in Brazilian HIV-1 epidemics at least 10 years after the subtype B. Notably, the BF recombinant emerged almost simultaneously with the introduction of subtype F in Brazil. Analysis of reverse transcriptase fragments indicated that the C subtype originated in the early 1990s, and the CB recombinant emerged 2 years after the appearance of subtype C. The high growth rate of BF recombinant possibly obscured the prevalence of the pure subtype F. In contrast, subtype C, although appearing 20 years after subtype B, was responsible for a well-defi ned epidemic. Nevertheless, the CB recombinant equally emerged rapidly after the introduction of the second parental (subtype C). Our results suggest that the outcome related to the recombinant profi le are probably infl uenced by the capacity of the newly arriving subtype to establish a critical number of infections before it recombines with the previous circulating subtype.

Epidemiologic and Evolutionary Trends of HIV-1 CRF31_BC-Related Strains in Southern Brazil

To evaluate the impact of HIV-1 CRF31_BC in the southern Brazilian HIV epidemic. Blood plasma from 284 patients was collected from July 2002 to January 2003 at 2 reference HIV/AIDS centers in southern Brazil. Viral protease and reverse transcriptase (RT) genomic regions were amplified by RT polymerase chain reaction, sequenced, and subtyped. Evolutionary analyses were performed to estimate the CRF31_BC most recent common ancestor and its population growth rate with BEAST version 1.3. CRF31_BC was responsible for 7.4% of infections. The average time of HIV diagnosis and the proportion of patients on antiretroviral treatment were shorter for CRF31_BC and subtype C than for subtype B. CRF31_BC was found as early as in 1990 in the Brazilian epidemic. Evolutionary analysis of CRF31_BC revealed that it appeared immediately after the introduction of subtype C in Brazil and has been growing at a similar rate as subtype C. CRF31_BC plays an important role in the HIV epidemic of southern Brazil, and its prevalence has increased throughout the years. This circulating recombinant form corresponds to approximately 25% of total HIV isolates in this region in 2004. Understanding the cause of this spread is important for public health strategies in Brazil and in Latin America.

Genetic Variability ofgagandenvRegions of HIV Type 1 Strains Circulating in Slovenia

The aim of this study was to investigate the genetic diversity of HIV-1 strains circulating in Slovenia. Proviral DNA isolated from peripheral blood mononuclear cells (PBMCs) of 20 randomly selected HIV-1-infected individuals was classified into subtypes by sequence-based phylogenetic analysis of the env (C2V3) and gag (p24) regions of the viral genome. The phylogenetic tree based on env C2V3 sequences showed that 15 of the 20 samples were subtype B, two A1, one F1, one CRF01_AE, and one CRF02_AG. The phylogenetic analysis of the gag gene yielded identical results expect for one sample that had a discordant subtype; it was identified as subtype A1 in the env and AE in the gag region. Our study confirmed that although subtype B predominates, other subtypes and circulating recombinant forms (CRFs) are also present in Slovenia. The high intrasubtype genetic diversity of subtype B sequences suggests a multiple introduction of subtype B strains into Slovenia.

Trends of HIV-1 molecular epidemiology in Venezuela: introduction of subtype C and identification of a novel B/C mosaic genome

Trends of HIV-1 molecular epidemiology in Venezuela: introduction of subtype C and identification of a novel B/C mosaic genome

Thermochemistry of organic and heteroorganic species. Part XII. Mono- and disubstituted acetylenes and ethynyl free radicals. New electronegativity scale

The first important result of the present work is that the enthalpy of formation Δ H° f (298 K) for ethynyl HCC free radical is now firmly established 123±2 kcal mol −1, whereas the most known higher experimental and theoretical values reflect its formation in excited states. For computation of the Δ H° f HCC radical, the most reliable results were obtained by applying isodesmic (formal) reactions CN+RCCH→RCN+ CCH. The isodesmic reaction HCC +RCCH→HCCH+RCC is recommended for computation of the Δ H° f for substituted RCC radicals. With systematic application of the enthalpic shift procedure for more than 20 classes of compounds and functions supplemented by introduction of sub-types and correction terms, this procedure now can be treated as a completed special methodology in molecules’ thermochemistry. Using this methodology, the novel or corrected Δ H° f values for about 120 monosubstituted RCCH acetylenes and 50 other compounds were calculated. For calculating the thermochemical properties of molecules and radicals the new electronegativity (EN) scale was elaborated which comprised for a moment about 210 groups. The general requirements for EN scales were formulated. Two scales EN and EN* were proposed for elements with vacant p- or d-orbitals. For the first time, the polarizability effect (PAZ) of a substituent in relation to EN is considered in detail for diverse types of chemical processes and parameters. It is shown that any EN scale can be applied in practice only for a narrow set of structurally similar substituents rather than as an absolute measure. The enthalpies of formation for 75 diacetylenes XCCX and XCCY are presented. Following the works of McKean on correlation of Δ ν is(CH) values in gas phase IR spectra with ΔBDEs (bond dissociation energies), the literature data on ν RCCH values were applied to calculate the enthalpies of formation for RCC free radicals. For the first time, the variable n cm −1/ kcal −1 for diverse types of C–H bonds directly linked with EN of C-atom was suggested: ∼9 cm −1 for alkane C-atom, ∼11 cm −1 for alkenes RC H CH 2 or RCHC H 2, ∼12 cm −1 for alkynes RCCH and ∼14 cm −1 for RCHO molecules. Analyzing the EN/PAZ interrelationship for particular case of RCC–H bond strengths, the Δ H° f values for 12 RCC radicals were found from literature ν RCC–H values and then calculated for additional 42 radicals together with ν RCCH frequencies. In all these calculations, the value 123 kcal mol −1 for Δ H° f for HCC radical was used. This value was further used to extract from published computed data (after their recalculation), an important thermochemical information on many unstable species (molecules, free radicals, carbenes) valuable for combustion processes. In general, serious inconsistency between our data and literature computed data on thermochemistry of acetylenes and substituted RCC radicals was found.

A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil.

To characterize the subtype C strains of HIV type 1 that circulate in Brazil, especially those originated from the southern part of the country. One hundred and twelve HIV-1-positive subjects had their plasma viral RNA extracted. Protease (PR) and reverse transcriptase (RT) genomic regions were polymerase chain reaction-amplified and sequenced for subtype determination. Subtype C strains were selected and compared to other strains of this subtype from the database, and specific amino acid signature patterns were searched. Brazilian subtype C viruses form a very strong monophyletic group when compared to subtype C viruses from other countries and presented specific signature amino acids. Recombinants between subtype C and B viruses have been documented in areas of co-circulation. The incidence of primary PR and RT inhibitor resistance mutations in drug-naïve subjects was observed. An increasing number of secondary resistance mutations was also seen, some of which are characteristic of subtype C-related sequences. Introduction of subtype C of HIV-1 in Brazil was likely a single event of one or a mixture of similarly related strains. Recombination between subtype C and B viruses is an ongoing process in the country. Primary and secondary drug resistance mutations were observed, although some of the secondary mutations could be associated with subtype C molecular signatures. Subtype-specific polymorphisms of PR and RT sequences found in this subtype C Brazilian variant might influence this emergence and have an impact on HIV treatment and on vaccine development in the country.

Genetic subtypes of HIV type 1 in Hungary.

We examined the diversity of HIV-1 subtypes in 11 adults from Hungary, using the heteroduplex mobility assay (HMA) and DNA sequencing. HMA results showed that HIV-1 gp120 sequences from 10 patients were of subtype B, whereas 1 patient, infected in Africa, carried a subtype C strain. DNA sequencing confirmed the HMA results and revealed a high intrasubtype diversity in the C2V3 region of env in different clade B isolates, which suggests multiple introduction of subtype B to Hungary. This study shows that subtype B is the predominant HIV-1 clade in Hungary.

Genetic analysis of human immunodeficiency virus in Abidjan, Ivory Coast reveals predominance of HIV type 1 subtype A and introduction of subtype G.

To better understand the molecular epidemiology of HIV genetic diversity in Abidjan, Ivory Coast, we performed a genetic analysis of 170 HIV-1-seropositive specimens representing newly diagnosed tuberculosis patients (n = 143) and women monitored in a mother-to-child transmission cohort study (n = 27). Preliminary screening with RFLP presumptively classified 162 (95.3%) of these as subtype A. The envelope region of 108 specimens was subtyped by sequence analysis: 102 (94.4%) were subtype A, 2 (1.9%) were subtype D, and 4 (3.7%) were subtype G. Subtyping gag and env regions of the genome suggested that five of the six nonsubtype A isolates exhibited a potentially mosaic structure. A comparative phylogenetic analysis of HIV-1 subtype A C2V3 from 27 Ivory Coast and 21 Ugandan sequences revealed a striking clustering among Ivory Coast variants, and an independent segregation from Ugandan subtype A. Despite independent clustering with other subtype A specimens, limited variability of the V3 loop apex was observed; the globally predominant V3 motif, GPGQ, represented 90.1% of the HIV-1 strains. This study demonstrates that clade A is the predominant HIV-1 subtype in HIV-seropositive individuals in Abidjan, Ivory Coast and that these strains are phylogenetically distinct from other subtype A strains observed in East Africa.

Genetic and phylogenetic analysis of HIV type 1 env subtypes in Ghana, west Africa.

The authors examined HIV-1 genetic variation among 19 HIV-1-infected people of mean age 34.5 years living in Accra Akwatia Kumasi and Ho in Ghana. One person was of unknown origin. Blood samples were collected between December 1993 and January 1996. 16 of the HIV-1 specimens clustered with members of subtype A but the clustering was not supported by 70% or more of the bootstrap tests. Two samples clustered with subtype D strains supported by 92.5% of the bootstrap trees and one sample clustered with subtype G strains supported by 96.2% of the bootstrap trees. For the Ghanaian specimens belonging to subtype A interhost distances at the nucleotide level averaged 14.9% of range 7.83-20.9%. The interhost distance between the two subtype D samples was 8.2%. A cocirculation of subtypes A D and G was identified in Akwatia.

Genetic variability of HIV type 1 in Bénin.

AIDS Research and Human RetrovirusesVol. 12, No. 15 Sequence Note: Genetic Variability of HIV Type 1 in BéninL. HEYNDRIC X, W. JANSSENS, M. ALARY, K. FRANSEN, K. VEREECKEN, S. COPPENS, B. WILLEMS, N. DAVO, A. GUÈDÈMÈ, E. BAGANIZI, J. JOLY, and G. VAN DER GROENL. HEYNDRIC XSearch for more papers by this author, W. JANSSENSSearch for more papers by this author, M. ALARYSearch for more papers by this author, K. FRANSENSearch for more papers by this author, K. VEREECKENSearch for more papers by this author, S. COPPENSSearch for more papers by this author, B. WILLEMSSearch for more papers by this author, N. DAVOSearch for more papers by this author, A. GUÈDÈMÈSearch for more papers by this author, E. BAGANIZISearch for more papers by this author, J. JOLYSearch for more papers by this author, and G. VAN DER GROENSearch for more papers by this authorPublished Online:15 Mar 2009https://doi.org/10.1089/aid.1996.12.1495AboutSectionsPDF/EPUB ToolsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetailsCited ByMolecular Epidemiology of Human Immunodeficiency Virus Type 1 Sub-Subtype A3 in Senegal from 1988 to 2001Journal of Virology, Vol. 78, No. 22Molecular characterization of a complex, recombinant human immunodeficiency virus type 1 (HIV-1) isolate (A/G/J/K/?): evidence to support the existence of a novel HIV-1 subtypeJournal of General Virology, Vol. 82, No. 10Genetic characterization of HIV type 1 and type 2 from Bissau, Guinea-Bissau (West Africa)Virus Research, Vol. 68, No. 1HIV prevalence and strain diversity in Gabon: the end of a paradoxAIDS, Vol. 14, No. 9GLOBAL EPIDEMIOLOGY OF SEXUALLY TRANSMITTED DISEASESSimplified Strategy for Detection of Recombinant Human Immunodeficiency Virus Type 1 Group M Isolates by gag/env Heteroduplex Mobility AssayJournal of Virology, Vol. 74, No. 1Genetic Analysis of Human Immunodeficiency Virus in Abidjan, Ivory Coast Reveals Predominance of HIV Type 1 Subtype A and Introduction of Subtype G Dennis L. Ellenberger, Danuta Pieniazek, John Nkengasong, Chi-Cheng Luo, Sushil Devare, Chantal Maurice, Mario Janini, Artur Ramos, Carol Fridlund, Dale J. Hu, Issa-Malick Coulibaly, Ehounou Ekpini, Stefan Z. Wiktor, Alan E. Greenberg, Gerald Schochetman, and Mark A. Rayfield5 July 2004 | AIDS Research and Human Retroviruses, Vol. 15, No. 1Molecular genotyping of HIV-1 in 61 patients with AIDS from Lom�, TogoJournal of Medical Virology, Vol. 57, No. 1Molecular genotyping of HIV-1 in 61 patients with AIDS from Lom�, TogoJournal of Medical Virology, Vol. 57, No. 1Sequence Note: A Novel Subtype A/G/J Recombinant Full-Length HIV Type 1 Genome from Burkina Faso ROBERT B. OELRICHS, CASSY WORKMAN, TIINA LAUKKANEN, FRANCINE E. McCUTCHAN, and NICHOLAS J. DEACON15 March 2009 | AIDS Research and Human Retroviruses, Vol. 14, No. 16Sequence Note: Genetic and Phylogenetic Analysis of HIV Type 1 Strains from Southern Ghana J.A.M. BRANDFUL, W.K. AMPOFO, W. JANSSENS, Y. ADU-SARKODIE, F. APEAGYEI, F. ANYOMI, S. AIDOO, N. YAMAMOTO, K. ISHIKAWA, T. SATA, and T. KURATA15 March 2009 | AIDS Research and Human Retroviruses, Vol. 14, No. 9Genetic Subtypes of HIV Type 1 and HIV Type 2 Strains in Commercial Sex Workers from Bamako, Mali MARTINE PEETERS, BRAHIMA KOUMARE, CLAIRE MULANGA, CECILE BRENGUES, BABY MOUNIROU, FLABOU BOUGOUDOGO, SOPHIE RAVEL, FREDERIC BIBOLLET-RUCHE, and ERIC DELAPORTE15 March 2009 | AIDS Research and Human Retroviruses, Vol. 14, No. 1The puzzle of HIV-1 subtypes in AfricaAIDS, Vol. 11, No. 6HIV-1 Subtypes and Recombinants Volume 12Issue 15Oct 1996 To cite this article:L. HEYNDRIC X, W. JANSSENS, M. ALARY, K. FRANSEN, K. VEREECKEN, S. COPPENS, B. WILLEMS, N. DAVO, A. GUÈDÈMÈ, E. BAGANIZI, J. JOLY, and G. VAN DER GROEN.Sequence Note: Genetic Variability of HIV Type 1 in Bénin.AIDS Research and Human Retroviruses.Oct 1996.1495-1497.http://doi.org/10.1089/aid.1996.12.1495Published in Volume: 12 Issue 15: March 15, 2009PDF download

Genetic variability of HIV type 1 in Kenya.

The AIDS epidemic is a rapidly growing problem in Nairobi where the seroprevalence in pregnant women increased from 4% in 1988 to over 10% in 1991. 22 HIV-1-seropositive pregnant women and 1 HIV-1-infected baby (K88) attending the Pumwani Maternity Hospital of Nairobi between 1990 and 1992 were studied as part of a cohort study of maternal risk factors in mother-to-child transmission. A 250-base pair (bp) fragment of the env gene encoding C2V3 was amplified mostly from DNA isolated from primary peripheral blood mononuclear cells and subsequently sequenced. The 23 newly determined HIV env sequences were aligned with 23 previously known sequences of HIV-1 isolates of diverse geographical origin and the sequence of the HIV-1-related chimpanzee isolate SIVcpz-gab on the basis of primary structure. Distance calculation tree construction and bootstrap analysis were realized with the software package TREECON. In the tree 8 major branches could be observed containing sequences representative of 8 different subtypes A B C D E F G and H besides the outlier group O. 19 of 23 Kenyan isolates clustered with D687 Z321 U455 and SF170 which were members of genetic subtype A. Phylogenetic analyses favored positioning of K976 as a divergent A subtype strain. For 4 strains (K29 K88 K98 and K112) the subtype A classification based on the gag gene was also observed on the basis of phylogenetic analysis of the C2V3 coding part of the env gene. The predicted amino acid sequence of the V3 region for these strains was also presented. The finding that among 23 HIV-1 isolates collected in Nairobi 19 were classified in subtype A versus 3 in subtype D together with a much larger variation between subtype A strains as compared to subtype D strains suggests an earlier introduction of a subtype A strain multiple introductions of subtype A strains and/or faster diversification of subtype A strains as compared to subtype D strains.

Subgroup G HIV type 1 isolates from Nigeria.

Nucleotide sequences were obtained for portions of the envelope and gag genes of 4 HIV-1 isolates from Nigeria. The gag gene sequences clustered with previously described gag sequences from Gabon Zaire and Taiwan which form the G clade of HIV-1. This documented for the first time the presence of subgroup G viruses in Nigeria. The env gene sequences were most closely related to env sequences reported from 2 isolates previously classified as gag subgroup G and with those 2 env sequences defined the subgroup G env genotype. Virus isolates were obtained by cocultivation of peripheral blood mononuclear cells (PBMCs) from Nigerian AIDS patients (isolates JV1018 and JP88) or healthy prostitutes (G3 and G9) with normal uninfected PBMCs (JV1083 JP88 and G3) or GEM-SS a T cell line (G9). Clones containing env and gag gene sequences were obtained by polymerase chain reaction amplification using DNA from these cultures. The region of gag amplified by primers SK37 and SK39 containing BamHI and KpnI sites respectively in 5 tails was cloned into the KpnI-BamHI site of pKSBluescript and sequenced. When the gag sequences from 2 of the Nigerian viruses were subtyped by weighted parsimony both viruses grouped with others of the gag G subgroup. A similar analysis of env sequences from all 4 Nigerian isolates showed that they were most closely related to 2 env sequences that had been assigned to env subgroup G. The Nigerian env sequences clustered more closely with each other than they did with the other 2 subgroup G viruses. Consensus of the inferred amino acid sequences of the 4 env genes showed that the V3 loop closely resembled the A to F consensus. 8 positions in the Nigerian consensus sequence appeared to be unique. However whether these are signature residues for Nigerian subgroup G isolates or for subgroup G isolates will require the characterization of more isolates.