HIV-1 latent reservoir size and diversity are stable following brief treatment interruption

BACKGROUND

The effect of a brief analytical treatment interruption (ATI) on the HIV-1 latent reservoir of individuals who initiate antiretroviral therapy (ART) during chronic infection is unknown.

METHODS

We evaluated the impact of transient viremia on the latent reservoir in participants who underwent an ATI and at least 6 months of subsequent viral suppression in a clinical trial testing the effect of passive infusion of the broadly neutralizing Ab VRC01 during ATI.

RESULTS

Measures of total HIV-1 DNA, cell-associated RNA, and infectious units per million cells (IUPM) (measured by quantitative viral outgrowth assay [QVOA]) were not statistically different before or after ATI. Phylogenetic analyses of HIV-1 env sequences from QVOA and proviral DNA demonstrated little change in the composition of the virus populations comprising the pre- and post-ATI reservoir. Expanded clones were common in both QVOA and proviral DNA sequences. The frequency of clonal populations differed significantly between QVOA viruses, proviral DNA sequences, and the viruses that reactivated in vivo.

CONCLUSIONS

The results indicate that transient viremia from ATI does not substantially alter measures of the latent reservoir, that clonal expansion is prevalent within the latent reservoir, and that characterization of latent viruses that can reactivate in vivo remains challenging.

TRIAL REGISTRATION

ClinicalTrials.gov NCT02463227FUNDING. Funding was provided by the NIH.

Characterization of HIV-1 Near Full-Length Proviral Genome Quasispecies from Patients with Undetectable Viral Load Undergoing First-Line HAART Therapy

Increased access to highly active antiretroviral therapy (HAART) by human immunodeficiency virus postive (HIV⁺) individuals has become a reality worldwide. In Brazil, HAART currently reaches over half of HIV-infected subjects. In the context of a remarkable HIV-1 genetic variability, highly related variants, called quasispecies, are generated. HIV quasispecies generated during infection can influence virus persistence and pathogenicity, representing a challenge to treatment. However, the clinical relevance of minority quasispecies is still uncertain. In this study, we have determined the archived proviral sequences, viral subtype and drug resistance mutations from a cohort of HIV⁺ patients with undetectable viral load undergoing HAART as first-line therapy using next-generation sequencing for near full-length virus genome (NFLG) assembly. HIV-1 consensus sequences representing NFLG were obtained for eleven patients, while for another twelve varying genome coverage rates were obtained. Phylogenetic analysis showed the predominance of subtype B (83%; 19/23). Considering the minority variants, 18 patients carried archived virus harboring at least one mutation conferring antiretroviral resistance; for six patients, the mutations correlated with the current ARVs used. These data highlight the importance of monitoring HIV minority drug resistant variants and their clinical impact, to guide future regimen switches and improve HIV treatment success.

Molecular Characteristics of the Envelope of Vertically Transmitted HIV-1 Strains from Infants with HIV Infection

Mother-to-child transmission (MTCT) of HIV offers a good opportunity to study the dynamics of early viral evolution in the host environment to which the virus has partially adapted. Such studies would throw light on the unique features of the infecting viruses, which will subsequently help to design preventive or therapeutic measures against the newly infecting and evolving strains of HIV. Therefore, we undertook a study to determine the genetic divergence of proviral envelope sequences from the HIV-infected infants (<2 years). Detailed analysis revealed unique features of potential N-linked glycosylation sites (PNGS) and their frequency of occurrence that built on the difference in length of the V1V2 region of the envelope sequences. Surprisingly, frequency of PNGS in the V5 region was found to revert rapidly, in about 75% of the sequences, which could surmise a fitness disadvantage in the variant forms. Further, a stable net charge was observed in the V2 and V3 regions prompting us to speculate on the established interaction of the transmitted variant with the integrin α4β7 receptor and R5 co-receptor, respectively. In brief, our observations suggest that differences in the length of the variable regions and variation in the frequency of PNGS in the envelope of the viruses obtained from very recently infected individuals in our population could be important characteristics of the unique quasispecies that is responsible for the spread of HIV in the early stages of infection in MTCT.

Multiple invasions of an infectious retrovirus in cat genomes

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of host germ-line cells. While most ERVs are defective, some are active and express viral proteins. The RD-114 virus is a replication-competent feline ERV, and several feline cell lines produce infectious RD-114 viral particles. All domestic cats are considered to have an ERV locus encoding a replication-competent RD-114 virus in their genomes; however, the locus has not been identified. In this study, we investigated RD-114 virus-related proviral loci in genomes of domestic cats, and found that none were capable of producing infectious viruses. We also found that all domestic cats have an RD-114 virus-related sequence on chromosome C2, termed RDRS C2a, but populations of the other RDRSs are different depending on the regions where cats live or breed. Our results indicate that RDRS C2a, the oldest RD-114-related provirus, entered the host genome before an ancestor of domestic cats started diverging and the other new RDRSs might have integrated into migrating cats in Europe. We also show that infectious RD-114 virus can be resurrected by the recombination between two non-infectious RDRSs. From these data, we conclude that cats do not harbor infectious RD-114 viral loci in their genomes and RD-114-related viruses invaded cat genomes multiple times.

The Staphylococci phages family: an overview

Due to their crucial role in pathogenesis and virulence, phages of Staphylococcus aureus have been extensively studied. Most of them encode and disseminate potent staphylococcal virulence factors. In addition, their movements contribute to the extraordinary versatility and adaptability of this prominent pathogen by improving genome plasticity. In addition to S. aureus, phages from coagulase-negative Staphylococci (CoNS) are gaining increasing interest. Some of these species, such as S. epidermidis, cause nosocomial infections and are therefore problematic for public health. This review provides an overview of the staphylococcal phages family extended to CoNS phages. At the morphological level, all these phages characterized so far belong to the Caudovirales order and are mainly temperate Siphoviridae. At the molecular level, comparative genomics revealed an extensive mosaicism, with genes organized into functional modules that are frequently exchanged between phages. Evolutionary relationships within this family, as well as with other families, have been highlighted. All these aspects are of crucial importance for our understanding of evolution and emergence of pathogens among bacterial species such as Staphylococci.

Characterization of a full-length endogenous beta-retrovirus, EqERV-beta1, in the genome of the horse (Equus caballus)

Information on endogenous retroviruses fixed in the horse (Equus caballus) genome is scarce. The recent availability of a draft sequence of the horse genome enables the detection of such integrated viruses by similarity search. Using translated nucleotide fragments from gamma-, beta-, and delta-retroviral genera for initial searches, a full-length beta-retrovirus genome was retrieved from a horse chromosome 5 contig. The provirus, tentatively named EqERV-beta1 (for the first equine endogenous beta-retrovirus), was 10434 nucleotide (nt) in length with the usual retroviral genome structure of 5'LTR-gag-pro-pol-env-3'LTR. The LTRs were 1361 nt long, and differed approximately 1% from each other, suggestive of a relatively recent integration. Coding sequences for gag, pro and pol were present in three different reading-frames, as common for beta-retroviruses, and the reading frames were completely open, except that the env gene was interrupted by a single stopcodon. No reading frame was apparent downstream of the env gene, suggesting that EqERV-beta1 does not encode a superantigen like mouse mammary tumor virus (MMTV). A second proviral genome of EqERV-beta1, with no stopcodon in env, is additionally integrated on chromosome 5 downstream of the first virus. Single EqERV-beta1 LTRs were abundantly present on all chromosomes except chromosome 24. Phylogenetically, EqERV-beta1 most closely resembles an unclassified retroviral sequence from cattle (Bos taurus), and the murine beta-retrovirus MMTV.

Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans

HERV-K113 and HERV-K115 have been considered to be among the youngest HERVs because they are the only known full-length proviruses that are insertionally polymorphic and maintain the open reading frames of their coding genes. However, recent data suggest that HERV-K113 is at least 800,000 years old, and HERV-K115 even older. A systematic study of HERV-K HML2 members to identify HERVs that may have infected the human genome in the more recent evolutionary past is lacking. Therefore, we sought to determine how recently HERVs were exogenous and infectious by examining sequence variation in the long terminal repeat (LTR) regions of all full-length HERV-K loci. We used the traditional method of inter-LTR comparison to analyze all full length HERV-Ks and determined that two insertions, HERV-K106 and HERV-K116 have no differences between their 5′ and 3′ LTR sequences, suggesting that these insertions were endogenized in the recent evolutionary past. Among these insertions with no sequence differences between their LTR regions, HERV-K106 had the most intact viral sequence structure. Coalescent analysis of HERV-K106 3′ LTR sequences representing 51 ethnically diverse individuals suggests that HERV-K106 integrated into the human germ line approximately 150,000 years ago, after the emergence of anatomically modern humans.

Compartmentalization of small ruminant lentivirus between blood and colostrum in infected goats

The compartmentalization of small ruminant lentivirus (SRLV) subtype A (Maedi-Visna virus) and B (caprine arthritis-encephalitis virus) variants was analyzed in colostrum and peripheral blood mononuclear cells of four naturally infected goats. Sequence analysis of DNA and RNA encompassing the V4-V5 env regions showed a differential distribution of SRLV variants between the two compartments. Tissue-specific compartmentalization was demonstrated by phylogenetic analysis in three of the four cases. In these animals colostrum proviral sequences were clustered relative to the blood viral sequences. In one goat, the blood and colostrum-derived provirus sequences were intermingled, suggesting trafficking of virus between the two tissues or mirroring a recent infection. Surprisingly, the pattern of free virus variants in the colostrum of all animals corresponded only partially to that of the proviral form, suggesting that free viruses might not derive from infected colostral cells. The compartmentalization of SRLV between peripheral blood and colostrum indicates that lactogenic transmission may involve specific viruses not present in the proviral populations circulating in the blood.

Human immunodeficiency virus type 1 drug resistance mutations in peripheral blood mononuclear cell proviral DNA among antiretroviral treatment-naive and treatment-experienced patients from Pune, India

The prevalence of HIV drug resistance (HIVDR) mutations in the HIV protease (PR) and reverse transcriptase (RT) genes was estimated from peripheral blood mononuclear cells (PBMCs) in a study population of 25 antiretroviral (ARV) therapy-naive and 50 ARV-experienced chronically infected patients from Pune city, Maharashtra State, western India. Of the 75 study HIV-1 sequences, 73 belonged to subtype C and 2 to subtype A1. On phylogenetic analysis, the study subtype C sequences sub clustered randomly with different Indian and non-Indian subtype C sequences, emphasizing the HIV-1 subtype C pol gene diversity. The heterosexual route was the most common route of transmission (74.67%). There were no observable HIVDR mutations in ARV-naive patients. The ARV-experienced patients had a history of exposure to nucleoside reverse transcriptase inhibitor and nonnucleoside reverse transcriptase inhibitor combinations. At least one HIVDR mutation in RT was observed in 29 (80.55%) of ARV-experienced patients with evidence of failing therapy. M184V was the most common observed HIVDR mutation. No PR major mutations were observed among ARV-experienced patients. A higher prevalence of proviral HIVDR mutations in PBMCs was associated with irregular adherence to therapy (p < 0.05) and HIV-1 RNA levels > 1000 copies/ml (p < 0.001).

Early archives of genetically-restricted proviral DNA in the female genital tract after heterosexual transmission of HIV-1

OBJECTIVES AND METHOD

In order to characterize human immunodeficiency virus type 1 (HIV-1) variants that are transmitted in women via heterosexual intercourse, the env V1-V3 sequences of HIV-1 provirus (DNA) and free virus (RNA) in paired samples of blood and cervicovaginal secretions of untreated chronically and primary infected African women were compared.

RESULTS

Env RNA sequences retrieved from plasma and genital compartments formed a single cluster in primary infection. In contrast, env RNA sequences from these two compartments were distinct in chronically infected women. Analysis of proviral DNA of primary infected women showed that most HIV-1 sequences derived from the genital epithelia form independent clusters from HIV-1 sequences of DNA from peripheral blood mononuclear cells and RNA recovered from plasma and genital secretions. Similarly, the analysis of proviral DNA in the genital compartment of chronically infected women showed the persistence of genetically-restricted cluster of HIV-1.

CONCLUSIONS

These observations indicate that a viral subpopulation is archived as proviral DNA in the female genital tract early in primary infection, and suggest that HIV-1 variants from the male donor are selected in the female mucosal site during male to female transmission of HIV-1.

Investigating signs of recent evolution in the pool of proviral HIV type 1 DNA during years of successful HAART

In order to shed light on the nature of the persistent reservoir of human immunodeficiency virus type 1 (HIV-1), we investigated signs of recent evolution in the pool of proviral DNA in patients on successful HAART. Pro-viral DNA, corresponding to the C2-V3-C3 region of the HIV-1 env gene, was collected from PBMCs isolated from 57 patients. Both "consensus" (57 patients) and clonal (7 patients) sequences were obtained from five time points spanning a 24-month period. The main computational strategy was to use maximum likelihood to fit a set of alternative phylogenetic models to the clonal data, and then determine the support for models that imply evolution between time points. Model fit and model-selection uncertainty was assessed using the Akaike information criterion (AIC) and Akaike weights. The consensus sequence data was also analyzed using a range of phylogenetic techniques to determine whether there were temporal trends indicating ongoing replication and evolution. In summary, it was not possible to detect definitive signs of ongoing evolution in either the bulk-sequenced or the clonal data with the methods employed here, but our results could be consistent with localized expression of archival HIV genomes in some patients. Interestingly, stop-codons were present at the same two positions in several independent clones and across patients. Simulation studies indicated that this phenomenon could be explained as the result of parallel evolution and that some sites were inherently more likely to evolve into stop codons.

Characterization of hortulanus endogenous murine leukemia virus, an endogenous provirus that encodes an infectious murine leukemia virus of a novel subgroup

Simple retroviruses present a unique opportunity for examining the host-virus relationship. Following exogenous infection and integration into the germ line, copies of these viruses can become fixed within the genome. The resulting endogenous proviral "fossils" represent a record of past retroviral infections and forms. Previous work in our laboratory has been directed at dissecting the extensive nonecotropic murine leukemia virus content of the mouse genome. One such provirus, hortulanus endogenous murine leukemia virus (HEMV), found in a single copy in the genome of Mus spicilegus, was remarkable for characteristics that suggested that it was ancient and related to the hypothetical common ancestor of murine leukemia viruses (MLVs) and other gammaretroviral species. In the present study, we have analyzed its functional properties. Transfection of a molecular clone of the HEMV provirus into mouse-derived cell lines revealed that it is replication competent. Furthermore, host range and interference studies revealed a strictly ecotropic host range and the use of a receptor distinct from those used by other classical MLVs. The identity of nucleotide sequence of the long terminal repeats (LTRs) further suggested that HEMV is a relatively recent insertion into the M. spicilegus genome at the distal end of chromosome 7. Although unique to M. spicilegus, its presence in a homozygous state in three individuals obtained from different regions implies that it has been present long enough to become fixed in this species. Exhaustive phylogenetic analysis of all regions of the HEMV genome supported the previously assigned ancestral position of HEMV relative to other MLV-related viruses. Thus, HEMV is a relatively recent introduction into the Mus germ line but is representative of a relatively ancestral MLV group.

Reliable Classification and Recombination Analysis of Porcine Endogenous Retroviruses

Prevention of cross-species infection with porcine endogenous retroviruses (PERV) is crucial for xenotransplantation. Previous studies described the potential risk of infection for the PERV gamma1 subfamilies A, B and C. Replication competent PERV gamma1 proviruses designated to a particular subfamily and hybrid viruses originating from retroviral recombination events between the subfamilies were observed. Future pig genome sequencing projects will reveal multiple novel PERV proviruses from additional breeds and animals. Evaluation of these viral genomes has to be carried out to assess the potential risk of retroviral cross-species infection. In this study, we tested common sequence comparison methods for the classification of PERV sequences and the detection of hybrid clones. The examination of the polymorphic nucleotide positions was found to be the most suitable procedure. We describe a fast and simple method using bioinformatic software tools which can also be applied to analogous analyses of other viral genomes.

Multiplicity of human immunodeficiency virus infections in lymphoid tissue

Human immunodeficiency virus type 1 (HIV-1)-infected splenocytes in humans were recently shown to harbor three to four proviruses per cell on average (A. Jung et al., Nature 418:144, 2002). However, the mechanisms that lead to such extensive multiple infections are not understood. Here, we find by using mathematical analysis that two mechanisms quantitatively capture the distribution of proviral genomes in HIV-1-infected splenocytes, one where multiple genomes are acquired one at a time in a series of sequential infectious contacts of a target cell with free virions and infected cells, and the other where cell-to-cell transmission of multiple virions or genomes results from a single infectious contact of a target cell with an infected cell. The two mechanisms imply different genetic diversities of proviruses within an infected cell and therefore different rates of emergence of drug resistance via recombination.

Higher Human T Lymphotropic Virus (HTLV) Provirus Load Is Associated with HTLV‐I versus HTLV‐II, with HTLV‐II Subtype A versus B, and with Male Sex and a History of Blood Transfusion

BACKGROUND

High human T lymphotropic virus (HTLV)-I provirus load (VL) has been associated with an increased risk of HTLV-associated myelopathy, but little is known about variation in HTLV-I or -II VLs by demographic characteristics and risk behaviors.

METHODS

We measured HTLV-I and HTLV-II VLs in a large cohort of 127 HTLV-I-seropositive and 328 HTLV-II-seropositive former blood donors, by use of real-time polymerase chain reaction using tax primers. Multivariable linear regression was used to control for confounding by relevant covariates.

RESULTS

The mean VLs were 3.28 log(10) copies/10(6) peripheral blood mononuclear cells (PBMCs) (range, 0.5-5.3 log(10) copies/10(6) PBMCs) for HTLV-I and 2.60 log(10) copies/10(6) PBMCs (range, 0.05-5.95 log(10) copies/10(6) PBMCs) for HTLV-II (P<.0001). HTLV-II VLs were higher in those subjects with subtype A infection (mean, 2.82 log(10) copies/10(6) PBMCs) than in those with subtype B infection (mean, 2.29 log(10) copies/10(6) PBMCs) (P=.005). Higher HTLV-I VL was associated with previous receipt of a blood transfusion (P=.04), and lower HTLV-II VL was associated with female sex (P=.007). These associations persisted in virus-specific multivariate linear regression models controlling for potential confounding variables.

CONCLUSIONS

VL was significantly higher in HTLV-I than in HTLV-II infection and was higher in HTLV-II subtype A than in HTLV-II subtype B infection. Chronic HTLV VLs may be related to the infectious dose acquired at the time of infection, with higher VLs following acquisition by blood transfusion and lower VLs following sexual acquisition.

Provirus variants of bovine leukemia virus in naturally infected cattle from Argentina and Japan

A serologic subgroup of bovine leukemia virus (BLV) has not been identified, whereas genetic diversity among BLVs has been reported by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP). To investigate the distribution of BLV provirus variants, 42 isolates from Argentina and Japan were examined by nested PCR for a segment of the env gene, followed by DNA sequencing. The nucleotide sequences were compared with other previously characterized BLV variants from different geographical areas (Belgium, France, Italy, North America, Australia, Japan and Argentina). The majority of analyzed segments had a tendency for nucleotide substitution without changing the amino acid. The constructed phylogenetic tree showed the relations and differences between proviruses and within each one. Most of the samples in Argentina formed one cluster. The samples in Japan, except one, also formed one cluster and some of them showed high homology with the isolates from Australia and the USA. Considering the sequence analysis of env PCR products of all Japanese and Argentine samples and comparing them with the other previously isolated sequences, the variation was up to 3.5% and was characterized geographically in each area.

Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes

In a previous search based on the envelope gene, we had identified two related proviral elements that could not be included in identified ERV families. An in silico database screening associated with an in vivo polymerase chain reaction search using primers in the reverse transcriptase domain, now allowed identification of a series of related elements, found at a limited number in simians. A phylogenetic analysis led to their inclusion in a new family of endogenous retroviruses with limited expansion, which we named ERV-Fc, and which is part of the enlarged ERV-F/H family. The human genome comprises only six HERV-Fc, among which two possess full-length coding envelope genes. A complete provirus was identified in the baboon, also disclosing a fully open envelope gene. Cloning of the sites orthologous to the envelope-coding human proviruses demonstrated presence of the integrated proviruses in chimpanzee and gorilla, but not in orangutan. For the baboon element, the orthologous locus was found empty even in the phylogenetically most closely related macaque, again suggesting, together with the complete identity of its LTRs, "recent" integration. The data presented are compatible with an evolutionary scheme in which the ERV-Fc proviruses would be the endogenous traces of an active retroviral element, possibly acting as an infectious retrovirus with low endogeneization potency, with evidence for integrations at two distinct periods of primate evolution.

Insertional polymorphisms of full-length endogenous retroviruses in humans

Human endogenous retrovirus K (HERV-K) is distinctive among the retroviruses in the human genome in that many HERV-K proviruses were inserted into the human germline after the human and chimpanzee lineages evolutionarily diverged [1, 2]. However, all full-length endogenous retroviruses described to date in humans are sufficiently old that all humans examined were homozygous for their presence [1]. Moreover, none are intact; all have lethal mutations [1, 3, 4]. Here, we describe the first endogenous retroviruses in humans for which both the full-length provirus and the preintegration site alleles are shown to be present in the human population today. One provirus, called HERV-K113, was present in about 30% of tested individuals, while a second, called HERV-K115, was found in about 15%. HERV-K113 has full-length open reading frames (ORFs) for all viral proteins and lacks any nonsynonymous substitutions in amino acid motifs that are well conserved among retroviruses. This is the first such endogenous retrovirus identified in humans. These findings indicate that HERV-K remained capable of reinfecting humans through very recent evolutionary times and that HERV-K113 is an excellent candidate for an endogenous retrovirus that is capable of reinfecting humans today.

[Defective proviruses of the human T-cell leukemia virus: structure and classification]

Peripheral blood mononuclear cells of 24-70% individuals infected with HTLV-1 contain defective proviruses (dp) in addition to the full size ones. Most of them remain silent lacking regions sufficient for viral genes transcription except those activated under cell promoter or retaining viral open reading frames (orfs). It is still unclear whether these proviruses are associated with the development of T-cell leukemia in adults, tropic spastic paresis, or myelopathy. Classification of previously reported dp is presented, their origin and possible function in human HTLV-1 associated diseases are discussed.

Characterization of VPI pathogenicity island and CTXphi prophage in environmental strains of Vibrio cholerae

Environmental isolates of Vibrio cholerae of eight randomly amplified polymorphic DNA (RAPD) fingerprint types from Calcutta, India, that were unusual in containing toxin-coregulated pilus or cholera toxin genes but not O1 or O139 antigens of epidemic strains were studied by PCR and sequencing to gain insights into V. cholerae evolution. We found that each isolate contained a variant form of the VPI pathogenicity island. Distinguishing features included (i) four new alleles of tcpF (which encodes secreted virulence protein; its exact function is unknown), 20 to 70% divergent (at the protein level) from each other and canonical tcpF; (ii) a new allele of toxT (virulence regulatory gene), 36% divergent (at the protein level) in its 5' half and nearly identical in its 3' half to canonical toxT; (iii) a new tcpA (pilin) gene; and (iv) four variant forms of a regulatory sequence upstream of toxT. Also found were transpositions of an IS903-related element and function-unknown genes to sites in VPI. Cholera toxin (ctx) genes were found in isolates of two RAPD types, in each case embedded in CTXphi-like prophages. Fragments that are inferred to contain only putative repressor, replication, and integration genes were present in two other RAPD types. New possible prophage repressor and replication genes were also identified. Our results show marked genetic diversity in the virulence-associated gene clusters found in some nonepidemic V. cholerae strains, suggest that some of these genes contribute to fitness in nature, and emphasize the potential importance of interstrain gene exchange in the evolution of this species.

Identification of different BLV provirus isolates by PCR, RFLPA and DNA sequencing

A first attempt for the investigation of molecular epidemiology of BLV was carried out. PCR amplicons of a part of the env gene of BLV isolated from 309 cattle of different geographical origin were compared with known BLV env sequences. Using RFLPA most of the PCR products can be assigned to the Australian, the Japanese or the Belgian subgroup. A phylogenetic tree resulting from the comparison of the sequences of these env fragments demonstrates the relations and differences between and within the subgroups.

Changing epidemiology of HIV type 1 infections in India: evidence of subtype B introduction in Bombay from a common source

India has experienced multiple introductions of diverse HIV-1 subtypes A, B, C, and E, along with subtype B of HIV-2 between the 1980s and early 1990s. In this study, we have carried out a molecular investigation of 21 heterosexually and vertically acquired HIV-infected individuals from the New Bombay area, who tested positive for HIV-1 by commercial enzyme-linked immunosorbent assay (ELISA) and Western blot assay. We have sequenced the proviral DNA segments from the uncultured PBMCs in the hypervariable env V(3) region (286 bp) and a full-length vpr gene (291 bp). Overall, phylogenetic clustering of all Indian strains and also their clustering with subtype B strains were evident from both V(3)- and vpr gene-based trees, strongly supporting their recent introduction from a common source. This is the first report on subtype B introduction in Bombay, a region where subtype C predominates. Overall, these subtype B strains from Bombay shared genetic closeness with subtype B strains from Europe, the United States, and Asia.

Infection of the CD45RA+ (naive) subset of peripheral CD8+ lymphocytes by human immunodeficiency virus type 1 in vivo

To investigate the mechanism and functional significance of infection of CD8+ lymphocytes by human immunodeficiency virus type 1 (HIV-1) in vivo, we determined frequencies of infection, proviral conformation, and genetic relationships between HIV-1 variants infecting naive (CD45RA+) and memory (CD45RO+) peripheral blood CD4+ and CD8+ lymphocytes. Infection of CD3+ CD8+ CD45RA+ cells was detected in 9 of 16 study subjects at frequencies ranging from 30 to 1,400 proviral copies/10(6) cells, more frequently than CD3+ CD8+ lymphocytes expressing the RO isoform of CD45 (n = 2, 70 and 260 copies /10(6) cells). In agreement with previous studies, there was no evidence for a similar preferential infection of CD4+ naive lymphocytes. Proviral sequences in both CD4+ and CD8+ lymphocyte subsets were complete, as assessed by quantitation using primers from the long terminal repeat region spanning the tRNA primer binding site. In six of the seven study subjects investigated, variants infecting CD8+ lymphocytes were partially or completely genetically distinct in the V3 region from those recovered from CD4+ lymphocytes and showed a greater degree of compartmentalization than observed between naive and memory subsets of CD4+ lymphocytes. In two study subjects, arginine substitutions at position 306, associated with use of the chemokine coreceptor CXCR4, were preferentially found in CD4 lymphocytes. These population differences may have originated through different times of infection rather than necessarily indicating a difference in their biological properties. The preferential distribution of HIV-1 in naive CD8+ lymphocytes indeed suggests that infection occurred early in T-lymphocyte ontogeny, such as during maturation in the thymus. Destruction of cells destined to become CD8+ lymphocytes may be a major factor in the decline in CD8+ lymphocyte frequencies and function on disease progression and may contribute directly to the observed immunodeficiency in AIDS.

Characterization of the three HERV-H proviruses with an open envelope reading frame encompassing the immunosuppressive domain and evolutionary history in primates

The HERV-H family is one of the largest human endogenous retrovirus families, with approximately 1000 elements. Using a direct coupled in vitro transcription/translation approach (PTT for protein truncation test) and an extended series of primers on human genomic DNA, on monochromosomal hybrids and on a BAC library, we could demonstrate that there are only three envelopes with a large open reading frame encompassing the immunosuppressive (ISU) domain, corresponding to 62-, 60-, and 59-kDa potential translational products. The associated proviruses, HERV-H/env62, HERV-H/env60, and HERV-H/env59 were sequenced together with their flanking DNA and mapped by FISH, and their entry times within the primate lineage were determined. Analysis of the LTR sequences revealed numerous recombinational and/or homogenization events in the course of evolution, with divergences between 5' and 3' LTRs higher than expected for a simple time-dependent genetic drift. PTT analyses further revealed that the three large envelopes in humans are prematurely stopped in the majority of primates, and sequencing of the largest envelope gene, from HERV-H/env62, in five human individuals revealed two polymorphic sites. The results are consistent with the absence of a strong selective pressure for the conservation of a functional envelope gene of possible benefit for the host, but do not exclude somatic effects possibly associated with the immunosuppressive domain carried by these genes.

Endogenous retroviruses and the human germline

The human genome is rife with the proviral remains of many ancient retroviruses. The past year has seen significant progress in understanding the structure, distribution and potential function of many of these elements. Although hypotheses concerning the potential effects of these elements are common, however, incisive experiments to test any functions remain much less so.

Genomic relatedness of Staphylococcus aureus phages of the International Typing Set and detection of serogroup A, B, and F prophages in lysogenic strains

On the basis of HindIII-restriction digest analysis of genomic DNAs, the S. aureus bacteriophages of the International Typing Set were divided into five clusters designated as A, F, Ba, Bb, and Bc. The clusters A and F include all the phages of serogroups A and F and correspond to species 3A and 77 proposed by Ackermann and DuBow (1987). On the other hand, the phages of serogroup B were divided into three clusters designated as Ba, Bb, and Bc that differ significantly each from the other in their restriction patterns. The clusters Ba and Bb may represent two separate species, while the cluster Bc may include more than one phage species. For each of the phage serogroups A, B, and F, common HindIII-restriction fragments of phage 3A (1700 bp), of 53 (4060 bp), and of 77 (8300 bp) were used for the preparation of probes specific to the phages of serogroups A, B, and F. These probes were very effective, making it possible to detect up to three different prophages in a given lysogenic strain at the same time. Restriction enzyme maps of phages 3A, 53, and 77, each representing a different serogroup, were constructed. The restriction maps of phage 3A and that of phage 77 are linear, whereas that of phage 53 is circular and exhibits a circular permutation. DNAs of the phages of serogroups A and F have cohesive ends. On each restriction map, the sites corresponding to specific probes are indicated. The size of intact genomic DNA of all phages estimated by PFGE varies within the range of 41.5-46.2 kb.

Genome organization and phylogenetic distribution of a novel family of ancient murine endogenous proviruses with evidence for transposition-mediated proliferation

A new family of murine endogenous proviruses (VL6.0) is described here. The intact provirus is near 6 kb in length and shows a genomic organization of 5' LTR, gag, pol, env, and 3' LTR. The primer binding site (PBS) is that of a tRNA(gly). The lack of functional open reading frames and occurrence of significant gaps in most, if not all, members of this group show it to be ancient. Our estimate of copy number per haploid genome is 30+. Members of this group have been isolated from Mus musculus domesticus, M. m. casteneus, M. m. hortulanus, M. caroli, and M. spretus. The occurrence of these sequences throughout such diverse members of the genus Mus may indicate that the date of the original infection predated the divergence of the extant Mus lineages at around 2.5 million years ago. Analysis of gap (deletion/insertion) patterns indicates that these sequences may have proliferated within the Mus genome by a mechanism of reverse transcriptase-mediated transposition. As yet, there are no closely related murine retroviruses described. The closest mammalian retrovirus based on sequence similarity is from the miniature swine (Sus scrofa).

The detection of proviral DNA by semi-nested polymerase chain reaction and phylogenetic analysis of Czech Maedi-Visna isolates based on gag gene sequences

A semi-nested polymerase chain reaction (snPCR) for detecting proviral DNA of ovine lentivirus (OvLV) in peripheral blood mononuclear cells was developed. Primers for snPCR were situated within the gag gene of the Maedi-Visna virus (MVV) genome. A comparison between the snPCR and serological tests (agar gel immunodiffusion test, immunoblot) were performed using 98 ovine blood samples. Thirty (30.6%) of the 98 sheep examined had antibodies specific for the MVV. PCR showed 21 of them to be positive and nine seropositive animals to be PCR negative. Six of the 68 serologically negative sheep were found to be PCR positive, probably due to delayed seroconversion. The PCR amplification products of these six sheep were sequenced and subjected to phylogenetic analysis. The resulting phylogenetic tree of partial gag gene sequences confirmed that the ovine lentivirus genotype in the Czech Republic is more closely related to the prototype MVV isolates than to the caprine arthritis encephalitis viruses.

Proviral organization and sequence analysis of feline immunodeficiency virus isolated from a Pallas' cat

The nucleotide sequence and genomic organization have been determined for a highly cytopathic feline immunodeficiency virus (FIV) isolated from a Pallas' cat. The 9747-bp provirus of this virus, FIV-Oma, has typical lentivirus organization with LTRs, gag, pol, and env open reading frames (ORFs), putative vif and rev ORFs, and an ORF similar to ORF2/ORFA of domestic cat FIV isolates. Although the FIV-Oma provirus is 300 to 600 bp longer than other FIV proviruses, these additional bases are distributed throughout the genome. Phylogenetic analysis of a conserved region of the pol gene suggests that FIV-Oma is more closely related to some of the puma and lion lentiviruses than it is to domestic cat FIV isolates; however, many regions of the genome exhibit extensive nucleotide sequence divergence. None of the eight molecular proviral clones isolated from a genomic library are infectious, but we have constructed an infectious, cytopathic clone of FIV-Oma from subcloned and PCR-amplified fragments of these proviral clones. This clone will be useful for identifying the genetic determinants of FIV-Oma's biological activities.

[The identification of the genetic subtypes of HIV-1 circulating on the territory of Russia]

In this work the results of the genotyping of HIV strains obtained from 12 patients residing in Russia are presented. Proviral DNA from lysates of mononuclear cells was amplified with the use of primers, complementary to the conservative site of gene gag p7/p9 with the subsequent sequencing of the amplified material and phylogenetic analysis. 9 strains were classified with subtype B (most frequently occurring in Western countries), 2 of them being found closely related (probably, of African origin). In 2 patients infected from the same source the virus of unusual subtype F/1 was identified. This is the second case of the detection of this subtype in the world. One strain belonged to subtype G. in spite of the fact that in accordance with the epidemiological history only 3 patients got infection outside Russia, molecular epidemiological studies showed the genetic heterogeneity of the circulating strains and suggested the diversity of sources of the penetration of HIV infection to Russia.

Subtyping of human T-lymphotropic virus type I by amplification of long terminal repeat sequences and restriction fragment length polymorphism analysis in carriers with multiple transfusions

Five major subtypes of human T-lymphotropic virus type I (HTLV-I) have been proposed: cosmopolitan, Japanese, West African, Central African, and Melanesian. Based on nucleotide variations specific to particular subtypes, it was possible to genotype HTLV-I rapidly by restriction fragment length polymorphism (RFLP) studies following polymerase chain reaction (PCR). In this study, the restriction patterns of two LTR fragments were analyzed using eight restriction endonucleases (AvaI, Eco57I, BsoFI, NdeI, SacI, DraI, MaeII, and MaeIII). Genotyping of HTLV-I was done in nine patients with adult T-cell leukemia or HTLV-I-associated myelopathy/tropical spastic paraparesis, in three prostitutes, and in 19 carriers with multiple transfusion in Taiwan. The subtyping results of RFLP studies using these eight restriction endonucleases were in accordance with those of phylogenetic analysis. A substitution of G by A at nucleotide position 503, which creates the DraI site but suppresses the SacI site, was found not only in the Japanese subtype but also in a minority of the cosmopolitan subtype. A mutation near the position of subtype-specific nucleotide variations might suppress the restriction site and lead to unexpected restriction patterns. Amplification of more than one proviral fragment and RFLP studies with a group of appropriate restriction endonucleases may provide rapid and accurate genotyping of HTLV-I. More carriers are required to evaluate the possibility of mixed infection with different HTLV-I subtypes.

Typing human T-cell lymphotropic virus (HTLV-I and HTLV-II) by nested polymerase chain reaction: application to clinical specimens

Human T-cell lymphotropic virus type I and II provirus DNA was detected by polymerase chain reaction (PCR). MT-2 (HTLV-I infected), C3/44 Mo (HTLV-II infected) cell lines and peripheral blood mononuclear cells (PBMNC) from HTLV seropositive samples were used. The procedure consists of first amplification which detects both HTLV-I and HTLV-II, and a second amplification (nested-PCR) to discriminate between the two viruses and to improve sensitivity. Optimal conditions of MgCl2 concentration and annealing temperature were found for maximal amplification and specificity. This method was used for the amplification of conserved regions of pol and env genes. 1.5 pg of MT-2 and 5 pg of C3/44 Mo cell line DNAs were detected using nested-PCR and liquid hybridization in the pol system. The env system could detect 1.5 pg of MT-2 and 1.5 pg of C3/44 Mo cell lines DNAs using nested-PCR and liquid hybridization. The pol system can type both HTLV-I and HTLV-II in only two steps without the use of type-specific radiolabeled probes. Furthermore, this method can detect and discriminate the two viruses in one step PCR using the primers used in the nested-PCR. Nevertheless, there is a decrease in sensitivity of 100-fold. The results of five seropositive samples confirmed by Western blot are compared with PCR. PCR typed one of these samples as HTLV-I and the rest as HTLV-II. This technique is useful in cases such as window period, perinatal studies and when serologic results are not satisfactory.

Presence of multiple genetic subtypes of human immunodeficiency virus type 1 proviruses in Uganda

DNA sequences encoding the C2-V3 regions or the C2-V5 regions of the surface glycoprotein gp120 of the human immunodeficiency virus type 1 (HIV-1) were amplified by the polymerase chain reaction (PCR) from peripheral blood mononuclear cells obtained in 1990/1992 from 20 infected Ugandans. The PCR-amplified DNA was cloned into a phagemid vector and between 1 and 12 clones from each provirus were sequenced. The Ugandan proviruses were aligned into four subtypes (A, B, C, and D) by phylogenetic analysis of consensus nucleotide sequences for the C2-V3 regions. Analysis of the deduced amino acid sequences of the C2-V3 regions by a maximum parsimony program gave a similar phylogenetic relationship. The data indicated that phylogenetic analysis of nucleotide and/or amino acid sequences from the C2-V3 regions is a reliable method of subtype determination. The consensus amino acid sequence of the subtype A and D proviruses were almost identical to those of the Albert et al. group B and group A proviruses, respectively. The deduced amino acid sequences of the C2-V5 regions of six of these proviruses showed considerable diversity both between patients and within patients. The region varied in length between 234 and 243 amino acids and included deletions and repetitions, particularly in the V4 region.

HIV-1 proviral genotypes from the peripheral blood mononuclear cells of an infected patient are differentially represented in expressed sequences

The RNA genome of the human immunodeficiency virus type 1 (HIV-1) is established as proviral DNA in infected cells. Only some of these cells may actively produce the array of viral RNAs that support progeny virion production. In vivo expression of a subset of proviral genotypes could influence the experimental characterization of the viral quasispecies. We have explored the relationship between DNA and cDNA genotypes of the envelope gene by the molecular cloning and nucleotide sequencing of these templates from noncultivated peripheral blood mononuclear cells from an HIV-1-infected patient. Eleven proviral DNA and nine cDNA clones representing the V1-V3 region of gp120 were recovered and sequenced. The proviral group was more heterogeneous than the cDNA group by nucleotide sequence changes and V1 length polymorphisms. Deduced amino acid sequences from this data set showed that the two groups were distinct in primary structure, in the position of N-linked glycosylation sites, and in the net charge of the V3 loop. The V1-V2 region discriminated between the groups more strongly than the V3 region. The differential representation of HIV-1 envelope genotypes in the cDNA versus the proviral compartment may have important implications for the pathogenesis of disease and for the design of antiviral therapeutics.

Development of oligonucleotide primers and probes against structural and regulatory genes of human immunodeficiency virus type 1 (HIV-1) and their use for amplification of HIV-1 provirus by using polymerase chain reaction

The polymerase chain reaction is a powerful technique for amplifying a few copies of double-stranded genetic material to millions of copies in a few hours. The sensitivity and specificity of the polymerase chain reaction technique depend to some extent on the nucleotide sequences of the oligonucleotide primer pair used in the amplification. We report new oligonucleotide primers and probes which can be used for the amplification and detection of human immunodeficiency virus type 1 provirus sequences of not only structural but also regulatory genes. These primers are very sensitive and specific and can be used for the detection of African and North American strains of human immunodeficiency virus type 1.