Intrahost evolution of envelope glycoprotein and OrfA sequences after experimental infection of cats with a molecular clone and a biological isolate of feline immunodeficiency virus

Feline immunodeficiency virus (FIV) is a member of the genus Lentivirus and causes AIDS-like disease in its natural host, the cat. Like other lentiviruses, FIV displays a high degree of nucleotide sequence variability that is reflected in both the geographic distribution of the viruses and the different cat species that are infected. Although a lot of data on sequence variation at the population level is available, relatively little is known about the intrahost variation of FIV sequences. In the present study, cats were infected with either a biological isolate of FIV or a molecular clone that was derived from the same isolate, AM19. After infection, the cats were monitored for up to 3 years and at various time points sequences were obtained of virus circulating in the plasma. Regions of the env gene and the orfA gene were amplified, cloned and their nucleotide sequence analyzed. Furthermore, the extent of sequence variation in the original inocula was also determined. It was found that FIV is displaying relative little sequence variation during infection of its host, both in the env and the orfA gene, especially after infection with molecular clone 19k1. Although the extent of variation was higher after infection with biological isolate AM19, a large portion of these variant sequences was already present in the inoculum.     

Radioimmunoassay for the envelope glycoprotein of subgroup E avian leukosis-sarcoma viruses.

The envelope glycoprotein of subgroup E avian leukosis viruses (gpE) was purified from Rous-associated virus type 0 (RAV-0) and used in double-antibody competition radioimmunoassays (RIA) and radioimmune precipitations (RIP). When embryo extracts from various inbred lines of chickens were tested, the results of assays for chick helper factor (chf) and RAV-0 were in complete phenotypic agreement with those of RIA for gpE. The expression of genes at the gs and gp loci varied among inbred lines. Normal line 15I₅ embryos contained gpE but not group-specific (gs) antigens, whereas extracts from virus-free lines 15₁ and 6₁ contained both classes of antigen. Line 15_B embryo extracts were negative for both gpE and gs antigen. Soluble gpE was found in sera of all chf-positive chickens from RAV-0-free lines. Sera from adult line 15_B birds were categorized as: (1) positive for RAV-0 but negative for antibody; (2) negative for RAV-0 but positive for gpE and antibody to gpE; and (3) negative for RAV-0, antibody to gpE, and gpE. Evidence of antibody production was completely correlated in RIP of iodinated gpE and serum neutralizations of subgroup E virus. Results of RIP and gpE RIA indicated that half of the sera from nonviremic line 15_B chickens contained antibodies to gpE as well as gpE.     

Molecular localization of variable and conserved regions of pspA and identification of additional pspA homologous sequences in Streptococcus pneumoniae.

PspA is anchored to the surface of all pneumococci by the C-terminal end of the molecule. The N-terminal half of PspA is known to be serologically variable and to be able to elicit protective immune responses. Molecular analysis with DNA probes spanning different regions of pspA was carried out to identify homologous sequences among pneumococcal isolates. At high stringency, DNA probes derived from the 3'-half of pspA (encoding the C-terminal half of PspA) hybridized to all of 37 pneumococcal isolates tested, representing 20 capsular serotypes and 12 PspA serotypes. Most strains had two sequences highly homologous to this region of pspA. Using derivatives of strain Rx1, with insertion mutations in pspA, it was possible to identify the functional pspA sequence. At 50% stringency, the 3' pspA probes also detected lytA and additional sequences. lytA encodes autolysin and shares homology with the 3' portion of pspA. A probe derived from the 5'-half of pspA (encoding the N-terminal half of PspA) hybridized with only 75% of strains and generally detected only one of the two sequences recognized by the 3' probes. Thus, the 3'-half of pspA appears to contain more highly conserved sequences than the 5'-half of pspA and shares homology with several additional sequences, suggesting that the pneumococcus might make several proteins that interact with the surface by the same mechanism as PspA.     

Identification and characterization of conserved and variable regions in the neutralization vp2 gene of bluetongue virus

To determine the extent and nature of genetic variation among three serotypes of bluetongue virus (BTV), the nucleotide sequences of the outer capsid gene (L2) encoding the neutralization antigen (VP2) of serotypes BTV-11 and BTV-17 were determined. The predicted amino acids of the two proteins were then compared with that of BTV10(M. A. Purdy, H. Ghiasi, C. D. Rao, and P. Roy, 1985, J. Virol. 55, 826–830). The results indicated that although the three genes were closely related (70% conserved), the variation is extensive in comparison to the gene encoding the inner capsid polypeptide, VP3, which is 98% conserved in these serotypes(H. Ghiasi, M. A. Purdy, and P. Roy, 1985, Virus Res. 3, 181–190). Several regions with clustered amino acid substitution were identified. Based on predicted secondary structure and hydrophilicity, these variable regions represent potential antigenic sites. In contrast to the variable regions, other sequences and the overall VP2 structure (including cysteine, proline, and glycine residues) were highly conserved.     

Functional relationship between the matrix proteins of feline and simian immunodeficiency viruses

To investigate the functional relationship between the matrix (MA) proteins of feline and simian immunodeficiency viruses (FIV and SIV, respectively), we generated chimeric proviruses in which the MA-coding region of an SIV infectious molecular clone was partially or fully replaced by its FIV counterpart. Chimeric SIV proviruses containing the amino-terminal 36 residues or the central and carboxy-terminal regions of the FIV MA assembled into virions as efficiently as wild-type SIV. However, the resulting virions were noninfectious in single-cycle infectivity assays. Furthermore, a chimeric SIV provirus containing the entire FIV MA was found to be severely impaired in virion production due to inefficient membrane binding of the chimeric Gag polyprotein. Interestingly, the assembly defective phenotype of this chimeric Gag precursor could be reversed either by introducing the G31K/G33K double amino acid substitution in the FIV-derived MA domain or by coexpression with wild-type SIV Gag. Of note, a chimeric FIV provirus expressing the SIV MA not only assembled into particles as efficiently as wild-type FIV, but also replicated in feline T cells with wild-type kinetics. Our results thus provide novel information about the functional homology between the MA proteins of distantly related lentiviruses.     

Rapid evolution of two discrete regions of the caprine arthritis-encephalitis virus envelope surface glycoprotein during persistent infection

Five major regions of sequence diversity between strains (V1-V5) have been described in the caprine arthritis-encephalitis lentivirus (CAEV) envelope surface unit glycoprotein (SU). To determine which of these variable regions is important in persistent infection in vivo, we evaluated SU sequence diversity in five neutralization variants from two goats and proviral DNA from five additional goats infected with CAEV-63 for up to 7 years. Overall amino acid sequence divergence in the SU encoded by provirus and neutralization variants compared to parental CAEV-63 ranged from 1.1 to 4%. However, most of the amino acid substitutions and all of the deletions and insertions were present in two discrete regions designated HV1 and HV2. The HV2 region was variable in all neutralization variants and provirus sequences from most animals. This region overlapped the V4 domain of CAEV SU and the neutralization domain of the closely related ovine maedi-visna lentivirus. HV1 was located in a region of SU strictly conserved in all small ruminant lentivirus strains except CAEV-63. This region only varied in a subset of neutralization variants and proviruses, all derived from goats with arthritis. In contrast, sequences in the V1,V2,V3, and V5 regions were stable in neutralization variants and proviruses from infected goats, indicating that sequence diversity between strains in these regions is not due to selection of variants in persistently infected animals. Our results define two discrete regions of CAEV SU that undergo rapid sequence variation in persistently infected goats which may have important roles in virus-host interactions.     

Identification and antigenicity of the major envelope glycoprotein of lymphadenopathy-associated virus

The major envelope glycoprotein of the causative agent of Acquired Immune Deficiency Syndrome (AIDS) lymphadenopathy-associated virus (LAV) has been identified and characterized. The glycoprotein has an apparent molecular weight of 110,000-120,000 under denaturing conditions in polyacrylamide gel electrophoresis. Upon deglycosylation by a specific endoglycosydase, its size is reduced to 80,000. Cellular precursors of this glycoprotein have been detected with apparent molecular weight of 150,000 and 135,000. Nearly all AIDS and pre-AIDS patients have detectable antibodies against this viral glycoprotein.     

Computer predictions of functional,topogenic, and antigenic domains in human immunodeficiency virus-2 envelope glycoprotein

The gp160 of HIV-2 was studied with the aid of computer programs that provide the hydrophilicity, surface probability, flexibility, and antigenicity index of the amino-acid sequence in a polypeptide chain. Such analyses allow the identification of hydrophobic amino-acid domains in the polypeptide chain that may serve as putative proteolytic cleavage signals and putative antigenic domains. It was possible to define the function of hydrophobic domains in the polypeptide chain that serve as signals and amino-acid sequences involved in the transfer of the polypeptide through the cellular membrane by the cellular signal recognition protein (SRP) complex. By comparison to reported properties of HIV-1 gp160 and SIV_MAC gp160, it was possible to define antigenic domains in the loops of gp120 resulting from the reported interchain disulfide bonds defining putative antigenic domains specific for HIV-2.     

Identification and analysis of the gag-pol ribosomal frameshift site of feline immunodeficiency virus.

The pol genes of retroviruses are translated as gag-pol fusion proteins by ribosomal frameshifting within the gag-pol overlap region. During the ribosomal frameshift event, the gag open reading frame is shifted -1 nt to allow in-phase reading of the pol open reading frame. A consensus frameshift signal sequence of GGGAAAC within the gag-pol overlap region of feline immunodeficiency virus (FIV) has been identified followed by a sequence that has the potential for a pseudoknot tertiary structure. Using recombinant baculoviruses in which the frameshift occurs efficiently, the consensus sequence has been shown to be the site of the frameshift event. A mutation creating a termination codon just downstream of the putative frameshift signal sequence but upstream of the potential pseudoknot structure made a shorter gag product, but did not affect the efficiency of frameshifting. A mutation creating a termination codon just upstream of the putative frameshift signal made a shorter product and essentially abrogated frameshifting. Mutations in the first stem or the second stem in the potential pseudoknot structure severely reduced the frameshifting efficiency. Mutations which altered the length between the frameshift signal and the pseudoknot structure (the so-called spacer region) also reduced the frameshift efficiency. The insertion of a palindromic sequence, which could form a hairpin structure just upstream of the frameshift signal sequence, also affected the frameshifting. These results support the view that the ribosomal frameshift event in the FIV gag-pol region involves the identified signal sequence and appears to require the precisely positioned downstream sequence and indicated pseudoknot structure for efficient frameshifting.     

PCR-based study of conserved and variable DNA sequences of Tritrichomonas foetus isolates from Saskatchewan, Canada.

The protozoan parasite Tritrichomonas foetus causes infertility and spontaneous abortion in cattle. In Saskatchewan, Canada, the culture prevalence of trichomonads was 65 of 1,048 (6%) among 1,048 bulls tested within a 1-year period ending in April 1994. Saskatchewan was previously thought to be free of the parasite. To confirm the culture results, possible T. foetus DNA presence was determined by the PCR. All of the 16 culture-positive isolates tested were PCR positive by a single-band test, but one PCR product was weak. DNA fingerprinting by both T17 PCR and randomly amplified polymorphic DNA PCR revealed genetic variation or polymorphism among the T. foetus isolates. T17 PCR also revealed conserved loci that distinguished these T. foetus isolates from Trichomonas vaginalis, from a variety of other protozoa, and from prokaryotes. TCO-1 PCR, a PCR test designed to sample DNA sequence homologous to the 5' flank of a highly conserved cell division control gene, detected genetic polymorphism at low stringency and a conserved, single locus at higher stringency. These findings suggested that T. foetus isolates exhibit both conserved genetic loci and polymorphic loci detectable by independent PCR methods. Both conserved and polymorphic genetic loci may prove useful for improved clinical diagnosis of T. foetus. The polymorphic loci detected by PCR suggested either a long history of infection or multiple lines of T. foetus infection in Saskatchewan. Polymorphic loci detected by PCR may provide data for epidemiologic studies of T. foetus.     

Identification of a putative cellular receptor for feline immunodeficiency virus as the feline homologue of CD9.

A monoclonal antibody vpg15 has been identified which recognizes a putative cellular receptor for feline immunodeficiency virus (FIV). The antibody immunoprecipitates a single 24,000 MW species from feline cells. The molecular size and pattern of expression of the ligand for the vpg15 antibody displayed similarities to that of the human leucocyte differentiation antigen CD9. The reactivity of the vpg15 antibody was therefore compared with that of the anti-human CD9 antibody FMC56, an antibody which cross-reacts with feline cells. Expression of the vpg15 ligand correlated well with the reactivity of the FMC56 antibody on peripheral blood leucocytes and a panel of feline cell lines. Furthermore, the anti-human CD9 antibody reacted with murine fibroblast cells which had been transfected with high molecular weight feline DNA and immunoselected with the vpg15 antibody. FMC56 and vpg15 immunoprecipitated a similar 24,000 MW species from surface-iodinated feline cells and depletion of the vpg15 ligand from cell lysates resulted in a corresponding depletion of the FMC56 ligand. The data demonstrate that the vpg15 antibody recognizes the feline homologue of human CD9 and implicate feline CD9 as a cellular receptor for FIV.     

Phylogenetic analysis of the long terminal repeat of feline immunodeficiency viruses from Japan,Argentina and Australia

Summary The nucleotide sequences of the long terminal repeat of five Japanese, five Argentine and three Australian isolates of feline immunodeficiency virus (FIV) were determined and compared with those of isolates previously described. The results revealed that the Japanese isolates were found to cluster with nucleotide sequence similarity of 95.6%–99.4%. The Australian isolates also clustered with nucleotide sequence similarity of 97.2%–99.4%. The Argentine isolates formed two groups; the LP9 isolate is closely related to the Japanese isolates, whereas the LP1, LP3, LP20 and LP24 isolates are distant from both the Japanese and Australian isolates. From these results, FIV can be divided into three groups, namely: (I) the Californian, Australian and British isolates; (II) the Japanese isolates and one Argentine LP9 isolate; (III) the other Argentine isolates.     

Identification of antigenic regions in the GB hepatitis viruses GBV-A,GBV-B,and GBV-C

The genomes of two novel members of the Flaviviridae associated with GB agent hepatitis (GB viruses A and B) were cloned and sequenced recently. The genome of a third novel virus (GB virus C), related to but distinct from GB viruses A and B, has also been identified and characterized. Overlapping clones encompassing the large open reading frames of these three viruses have been expressed in E. coli as CTP:CMP-3-deoxy-D-manno-octulosonate cytidylyltransferase (CKS) fusion proteins. Bacterial lysates were subjected to Western blot analyses using sera from GB agent-infected tamarins and human sera from various individuals with or “at risk” for non-A, non-B, non-C, non-D, non-E hepatitis. Antigenic regions were identified in the putative NS3, NS4, and NS5 proteins from all three viruses. An antigenic region was also identified in the putative core protein of GB virus B. Many of the clones identified originally as encoding antigenic proteins were quite large. To map these regions more narrowly, smaller overlapping clones were generated by polymerase chain reaction (PCR), expressed as recombinant CKS fusion proteins and tested by Western blot. Additionally, a λgt11 expression library was generated from infectious tamarin sera and immunoscreened. These studies have identified at least three epitopes in GB virus A, five epitopes in GB virus B and four epitopes in GB virus C. © 1996 Wiley-Liss, Inc.     

Expression and characterization of a functional human immunodeficiency virus envelope glycoprotein in insect cells

Recombinant baculoviruses were used to express the gp160 envelope glycoprotein of the human immunodeficiency virus type 1 (HIV-1) and a truncated variant designated gp160(t) which lacks a transmembrane domain. Glycosylation, proteolytic cleavage, secretion, and biological activities of gp160 and gp160(t) 160(t) were studied in Spodoptera frugiperda cells. Both proteins were rapidly glycosylated and initially were found to be totally endo-beta-N-acetyl-D-glucosaminidase H (endo-H) sensitive. However, partial resistance to endo-H was gradually acquired by both molecules. gp160 was found to remain cell-associated, whereas gp160(t) was secreted into the culture medium in large amounts. A fraction of gp160 and gp160(t) appeared to be proteolytically cleaved, and a cleavage product corresponding in size to gp120 was identified in the culture medium. gp160(t) was found to interact specifically with CD4 receptors without any requirement for proteolytic cleavage. The gp160 protein was shown to be expressed on the surface of S. frugiperda cells by direct immunofluorescence. These surface molecules were biologically active, as demonstrated by their ability to induce syncytium formation when cocultivated with HeLa T4 cells.     

Characterization and nucleotide sequences of the variable regions of a monoclonal antibody against alpha-fetoprotein.

alpha-Fetoprotein (AFP) is a well-known tumor marker of hepatocellular carcinoma (HCC). Monoclonal antibodies against AFP possessing specific binding ability to HCC are potential candidates for immunoscintigraphy and immunotherapy. A new monoclonal antibody against AFP (0325-6-9) was isolated. Its specificity and targeting tumor ability were characterized by enzyme-linked immunosorbent assay (ELISA), cell immunostain and complement killing. These results suggest that 0325-6-9 is specific to hepatoma cells. The nucleotide sequences of variable regions of 0325-6-9 were determined by M13 dideoxynucleotide sequencing method. With the information of nucleotide sequence, this antibody then could be modified by recombinant technology for its usage in in vivo diagnosis and immunotherapy.     

Human immunodeficiency virus type 2 envelope glycoprotein: differential CD4 interactions of soluble gp120 versus the assembled envelope complex.

Utilizing a recombinant vaccinia expression system, we investigated the biological properties and CD4 receptor interactions of the envelope glycoproteins of a noncytopathic human immunodeficiency virus type 2 strain, termed HIV-2/ST, and a highly cytopathic variant derived from it. The efficiency and host cell range of syncytium formation by the recombinant glycoproteins of both viruses were highly restricted compared to those of prototypic strains of HIV (HIV-2/ROD or HIV-1/IIIB). However, the glycoprotein of cytopathic but not wild-type ST generated numerous large syncytia in the human T-cell line Sup T1 from which it was derived. A single cell line (Molt 4 clone 8) was permissive to fusion by both wild-type and cytopathic ST envelopes, but only the glycoprotein of cytopathic ST could be inhibited with a soluble form of the viral receptor CD4 (sCD4). While these results indicated major differences in the envelope glycoprotein-CD4 receptor interactions of wild-type versus cytopathic ST, direct and competition binding assays utilizing soluble external glycoprotein (SU) and sCD4 surprisingly revealed equivalent low binding affinity for both viruses. From these experiments we conclude that relevant biological properties (e.g., CD4 binding, cytopathic potential, and sCD4 neutralization) of HIV viruses which differ in their pathogenic potential are reflected in the sCD4 interactions of the assembled native envelope complex (as on cell or virion surfaces) but not the soluble SU glycoprotein.     

Recognition of helper T cell epitopes in envelope (E) glycoprotein of Japanese encephalitis, west Nile and Dengue viruses.

Helper T (Th) cell antigenic sites were predicted from the primary amino acid sequence (approximately 500 in length) of the envelope (E) glycoprotein (gp) of Japanese encephalitis (JE), West Nile (WN) and Dengue (DEN) I-IV flaviviruses. Prediction of Th epitopes was done by analyzing the occurrence of amphipathic segments, Rothbard-Taylor tetra/pentamer motifs and presence of alpha helix-preferring amino acids. The simultaneous occurrence of all these parameters in segments of E gp were used as criteria for prediction as Th epitopes. Only one cross reactive epitope was predicted in the C-terminal region of the E gp predicted segments of all flaviviruses analyzed. This region is one of the longest amphipathic stretch (approximately from 420 to 455) and also has a fairly large amphipathic score. Based on the predicted findings three selected peptides were synthesized and analyzed for their ability to induce in vitro T cell proliferative response in different inbred strains of mice (Balb/c, C57BL6, C3H/HeJ). Synthetic peptide I and II prepared from C-terminal region gave a cross reactive response to JE, WN and Den-II in Balb/c and C3H/HeJ mice. Synthetic peptide III prepared from N-terminal region gave a proliferative response to DEN-II in Balb/c strain only, indicating differential antigen presentation.