- Volume 77, Issue 8, 1996

A novel endogenous retrovirus (ERV) designated XA34 was isolated from a human glioma cDNA library using low stringency hybridization with an ERV-9 env probe. Southern blot hybridizations with human genomic DNA revealed the presence of approximately 16 genomic copies closely related to XA34. Sequencing of a 2303 bp cDNA clone of XA34 showed that it belongs to a new ERV family. The XA34 ERV has recombined with an ERV-9-like retrovirus resulting in a truncated ERV-9-like env region that ends with an Alul-like 3′ LTR. By using PCR, we isolated ≈ 940 bp pol fragments from three additional members of this family, XA35, XA36 and XA37. A fifth member, XA38, was isolated and sequenced as a 4729 bp genomic clone. The genomic XA38 clone spans from pol towards the 3′ flanking region. The XA38 virus contains a more cryptic env region. The XA38 env is truncated in the transmembrane region and the virus then ends with three Alu repeats. Southern blot studies with human, chimpanzee, orangutan and squirrel monkey DNA show the presence of the XA34 family in all these species. That both the New and Old World monkeys have this ERV family means that the integration and/or amplification in the primate germ-line of XA34 probably took place about 40–45 million years ago. The phylogeny and the closest relatives to ERV XA34 are discussed.

Human immunodeficiency virus type 1 (HIV-1) infection is frequently associated with concurrent infection by opportunistic pathogens, against which production of nitric oxide by host macrophages provides a first line of defence. We have investigated whether regulatory HIV-1 proteins, such as Tat, can modulate the activity of the inducible nitric oxide synthase (iNos) gene when expressed in stable transfectant lines of RAW264.7 cells. A bioassay for Tat, based on transactivation of an HIV-1 LTR-CAT reporter gene, allowed selection of Tat-expressing cells. Parental and Tat-expressing macrophages accumulated identical levels of nitrite following lipopolysaccharide (LPS) stimulation. Interferon γ (IFN-γ) stimulation however, resulted in reduced levels of nitrite accumulation as a direct consequence of Tat expression. Conditioned media from Tat-expressing cells reduced the level of nitrite accumulation in parental cells following IFN-γ stimulation but not stimulation with LPS. These results implicate HIV-1 Tat as a modulator of the IFN-γ-specific signal transduction pathways leading to iNos expression.

A macaque monkey infected with NM-3, a human immunodeficiency virus type 1 (HIV-1)-simian immunodeficiency virus strain mac (SIVmac) chimeric virus with env, rev, tat and vpu derived from HIV-1 and LTR, gag, pol, vif and vpx derived from SIVmac, became a long-term carrier (more than 2.8 years). This monkey produced neutralizing antibodies to the original NM-3 as well as to the parental HIV-1. The virus recovered at 116 weeks replicated more rapidly and productively in macaque peripheral blood mononuclear cells than the original virus. The recovered virus was not neutralized either by antibodies raised early in the monkey or by a neutralizing monoclonal antibody that recognizes the V3 loop of HIV-1 Env, whereas both the early antibodies and the monoclonal antibody neutralized the original NM-3. Analysis of the virus genomic population revealed a few common mutations in the V3 region that caused amino acid changes. These data are consistent with the hypothesis that the virus escaped from the early antibodies and that the observed mutations contributed to this, as with HIV-1-infected humans. The observed mutations could equally well be the result of adaptation to simian cells. These results suggest that the HIV-1-SIVmac chimeric virus will be useful for investigating genetic variation of HIV-1 env and alteration of biological properties in vivo in relation to the host immune response.

Human immunodeficiency virus type 1 (HIV-1) Gag-specific cytotoxic T lymphocyte (CTL) responses were studied in seven seropositive long-term asymptomatic individuals (CDC A1) with stable CD4 counts for more than 8 years. Using a set of partially overlapping peptides covering the whole Gag, five 15–20-mer peptides were found to contain CTL epitopes. Further characterization of these epitopes revealed a new HLA-A25-restricted CTL epitope in p24, p24203–212 ETINEEAAEW. This region of Gag is highly conserved in clades B and D of HIV-1. Naturally occurring amino acid sequences, containing p24203D (consensus HIV-1 clades A, C, F, G and H) or p24204I (HIV-2ROD) were not recognized by CTL recognizing the index peptide. No virus variants with mutations in this sequence were found in peripheral blood mononuclear cells from the HIV-1-infected individual concerned during the 8 year observation period, indicating that the virus had not escaped from the observed CTL response.

Recently, conflicting data have been published about the ability of antibodies which efficiently neutralize T cell-adapted human immunodeficiency virus type 1 (HIV-1) strains to neutralize primary HIV-1 strains in vitro and in vivo. Here we present data indicating that such antibodies fail to neutralize primary HIV-1 strains in vivo. To this end, a newly developed chimeric human-to-mouse model was used, in which several aspects of primary HIV-1 infection are mimicked. Poly- and monoclonal anti-bodies protected the grafted human cells, in a dose-dependent way, from infection with T cell-adapted HIV-1 in this system. A human monoclonal antibody specific for the CD4 binding domain that efficiently neutralizes HIV-1 IIIB in vitro did not protect the human graft from HIV-1 IIIB infection. None of the antibodies provided protection in the in vivo model against infection with primary HIV-1 strains, although they were able to neutralize these same strains in vitro.

Cells infected with two closely related isolates of bovine viral diarrhoea virus (BVDV), one cytopathic (CP) and one non-cytopathic (NCP), were examined for signs of apoptosis. The results from labelling DNA using terminal transferase and biotinylated dUTP and by observing oligonucleosomal-sized DNA fragmentation indicated that the CP strain of BVDV induced apoptosis in cell culture but the NCP strain did not. Induction of apoptosis correlated with infected cells undergoing apoptosis rather than interactions between infected and uninfected cells and the induction of apoptosis by CP BVDV was a dominant trait in cells co-infected with both types of virus.

The receptor proteins, MHVR1 (Bgp C or splice variant of mmCGM1 containing two ectodomains) and MHVR2 (mmCGM2) have been reported to be functional receptors for MHV, although there was a significant difference in their virus-binding activity as determined by virus overlay protein blot assay (VOPBA). To compare the receptor function of these proteins, their virus-binding capacities were tested by using soluble forms of the proteins which lacked the transmembrane and intracytoplasmic domains. To estimate the amounts of these proteins expressed, an epitope of influenza HA protein, for which specific monoclonal antibody was available, was used as a tag. Recombinant soluble MHVR1 and MHVR2, expressed in RK 13 cells using recombinant vaccinia virus were secreted into the culture fluids of infected cells expressing these proteins. The inhibitory effect on virus infectivity of MHVR1 was shown to be about 500-fold higher than that of MHVR2. A similar disparity was observed in virus binding by VOPBA. These two proteins worked as functional receptors when they were expressed on resistant BHK-21 cells. However, the efficiency of MHV infection in BHK-21 cells expressing MHVR1 was about 30-fold higher, as compared with those expressing MHVR2. These data show that the receptor function of MHVR1 was significantly higher than that of MHVR2 and suggests that the difference in susceptibility between SJL and BALB/c mice might be due to the specific receptor protein expressed in those animals.

The genome of the European brown hare syndrome virus (EBHSV), a calicivirus related to rabbit haemorrhagic disease virus (RHDV), was fully sequenced. It was 7442 bases long and contained two ORFs. In RHDV, the 5′ large ORF (ORF1) is predicted to encode a polyprotein precursor to the non-structural and capsid proteins. The small ORF (ORF2) encodes a predicted protein of 12 kDa. Alignment of sequences of EBHSV and RHDV showed 71% nucleotide identity; the changes were uniformly scattered over the whole genome. Minor differences could be detected when comparing two EBHSV sequences, indicating that EBHSV could vary to the same extent as RHDV. Four cleavage sites previously identified on the RHDV polyprotein were conserved in EBHSV. These sequencing data clearly show that EBHSV and RHDV share a similar genomic organization and confirm that EBHSV and RHDV are two distinct members within the family Caliciviridae.

Genetic and phylogenetic analysis of enteroviruses showed that in the 5′NCR enteroviruses formed three clusters: polioviruses (PVs), coxsackievirus A type 21 (CAV21), CAV24 and enterovirus type 70 (ENV70) formed one cluster; coxsackievirus B isolates (CBVs), CAV9, CAV16, ENV71, echovirus type 11 (EV11), EV12 and all partially sequenced echoviruses and swine vesicular disease virus (SVDV) belonged to another cluster and bovine enteroviruses (BEVs) formed the third cluster. In the capsid coding region five clusters were seen: PVs, CAV21 and CAV24 formed one cluster (PV-like); ENV70 formed a cluster of its own; all CBVs, CAV9, EV11, EV12 and SVDV formed the third cluster (CBV-like); CAV16, CAV2 and ENV71 belonged to the fourth cluster (CAV16-like) and BEVs formed their own cluster (BEV-like). In the 3′NCR the same clusters were seen as in the coding region suggesting a close association of the 3′NCR with viral proteins while the cellular environment may be more important in the evolution of the 5′NCR. Secondary structures were predicted in the 3′NCR, which showed two different patterns among the five clusters. A potential pseudoknot region common in all five clusters was identified. Although the BEV-like viruses formed a separate cluster in all genomic regions, in the coding region they seem to be phylogenetically related to the CAV16-like viruses.

Equine rhinoviruses (ERVs) are picornaviruses which cause a mild respiratory infection in horses. The illness resembles the common cold brought about by rhinoviruses in humans; however, the presence of a viraemia during ERV-1 infection, the occurrence of persistent infections and the physical properties are all more reminiscent of foot-and-mouth disease virus (FMDV). cDNA cloning and sequencing of the genomes of ERV-1 and ERV-2 between the poly(C) and poly(A) tracts showed that the serotypes are heterogeneous. Nevertheless, the genomic architecture of both serotypes is most similar to that of FMDV. Indeed, a comparison of the derived protein sequences of ERV-1 shows that their identity is greatest to FMDV. In contrast, most ERV-2 proteins are more related to encephalomyocarditis virus (EMCV) proteins than they are to FMDV or ERV-1. These results place ERV-1 alongside FMDV in the aphthovirus genus of the picornavirus family and indicate that this virus may serve as a model system for examining the biology of FMDV.

Immune sera were obtained from four rainbow trout that had survived natural infection by infectious haematopoietic necrosis virus (IHNV), and five monoclonal antibodies (MAbs) were prepared against a Korean isolate of IHNV, IHNV-PRT. These immune sera and MAbs were characterized in terms of IHNV-neutralizing properties and reactivity in Western blots with the viral proteins of IHNV-PRT. All five MAbs and four immune sera neutralized IHNV-PRT to various extents. Antibodies in these immune sera recognized two structural proteins of IHNV, G and M1, and one protein with a molecular mass of 90 kDa. Of the five MAbs, three (AB9, AF6 and AG6) recognized the IHNV G protein, and the other two (AB7 and BC2) recognized the 90 kDa protein. The 90 kDa protein was found to be a cellular protein constitutively expressed at low levels in fish cells and expression of this protein was augmented by infection with IHNV and heat shock. MAbs specific to four stress proteins, hsp60, hsp70, hsp90 and grp94, failed to bind to this 90 kDa protein. MAbs AB9 and AB7 reacted fairly broadly with six different IHNV strains. Together, these results indicate that (1) two IHNV proteins, G and M1, and a 90 kDa cellular protein are immunogenic, (2) G and the 90 kDa proteins contain neutralizing epitopes, and (3) the epitopes recognized by MAbs AB9 and AB7 are conserved among the six different IHNV strains.

A cotton rat (Sigmodon fulviventer) model of human parainfluenza virus type 3 (HPIV-3) infection was used to study patterns of HPIV-3 replication in naive and immune hosts. Growth curves revealed that nasal and pulmonary tissues of naive animals were semi-permissive for virus replication, with amounts of progeny virus proportional to inoculating doses. In naive animals there was a total eclipse in nasal tissues beginning 4 h after inoculation. By contrast, there was only partial eclipse of virus in pulmonary tissues, most pronounced at 1 h after inoculation. Immune animals demonstrated a delayed eclipse in pulmonary tissues upon rechallenge. Infection with very low doses of HPIV-3 induced complete protection against high-dose challenge in the absence of systemic neutralizing antibody, suggesting a significant role for other systemic or local immune effectors.

The RNA polymerase activity and PB1 binding of influenza virus PA mutants were studied using an in vivo-reconstituted polymerase assay and a two hybrid system. Deletions covering the whole PA protein abolished polymerase activity, but the deletion of the 154 N-terminal amino acids allowed PB1 binding, indicating that the PA protein N terminus is not absolutely required for this interaction. Further internal or C-terminal deletions abolished PB1 interaction, suggesting that most of the protein is involved in this association. As a novel finding we showed that a single amino acid insertion mutant, PAI672, was responsible for a temperature-sensitive phenotype. Mutant PAS509, which had a serine insertion at position 509, bound to PB1 like wild-type PA but did not show any polymerase activity. Over-expression of PAS509 interfered with the polymerase activity of wild-type PA, identifying PAS509 as a dominant negative mutant.

In the winter of 1989 and the spring of 1990, there were large outbreaks of respiratory disease in two swine herds in Nagasaki Prefecture, southern Japan. Serological surveillance indicated that the majority of swine possessed antibodies to swine influenza virus H1 haemagglutinin and neuraminidase of early H3N2 influenza virus strains. Eight viruses were isolated from swine that showed typical clinical symptoms of influenza. The haemagglutinin and neuraminidase of these isolates were closely related to those of swine H1N1 and early human H3N2 viruses, respectively. At least two types of haemagglutinin antigens, distinguished by two monoclonal antibodies, were involved in the outbreaks. Evolutionary analyses indicated that the haemagglutinin gene of the H1N2 reassortants was closely related to those of a recent swine lineage (A/sw/HK/1/74 and A/sw/Ehime/1/80 viruses). However, the neuraminidase genes of the H1N2 reassortants were similar to those of swine N2 viruses which in turn are related to early human H3N2 viruses. A comparison of partial nucleotide sequences revealed that the six other genes of A/sw/Nagasaki/1/89 were derived from those of swine H1N1 virus.

The complete nucleotide sequences of the small (S) genomic RNA segments of five California (CAL) serogroup bunyaviruses (two Inkoo virus strains, San Angelo virus, Serra do Navio virus, South River virus and Tahyna virus) were determined. In agreement with previously published data concerning CAL serogroup viruses, the nucleocapsid (N) and non-structural (NS s ) proteins were encoded in over-lapping open reading frames (ORFs). All N protein ORFs were 708 nucleotides in length and encoded a 235 amino-acid gene product. The NS s ORFs were either 279 or 294 nucleotides in length, which would encode 92 or 97 amino-acid proteins, respectively. Comparative analysis of the nucleotide sequences and amino acids corresponding to the nucleocapsid protein resulted in a predicted relationship among these viruses that generally agreed with those determined by serology. The only exception was Inkoo virus, where comparisons based on the S RNA sequence and partial M RNA sequence suggest that this virus is more similar to Jamestown Canyon virus of the Melao complex than it is to viruses such as Tahyna and La Crosse viruses of the California encephalitis complex.

Inkoo (INK) and Tahyna (TAH) viruses, European representatives of the California serogroup (CAL), genus Bunyavirus, family Bunyaviridae, are transmitted by mosquitoes and frequently infect man. The S segments of INK and TAH prototype strains were amplified, cloned and sequenced. INK S consists of 986 and TAH S of 977 nucleotides (nt) coding for a nucleocapsid protein of 235 amino acids (aa) and, in an overlapping reading frame, for a nonstructural protein of 92 or 97 aa, respectively. By S segment sequences and phylogenetic analysis INK was seen to be most closely related to Jamestown Canyon virus, isolated in the USA (92.4% nt and 96.6% aa identity), which is currently classified in a different subcomplex within the CAL viruses. TAH was genetically closest to Lumbo virus, isolated in Mozambique (89.0% nt and 94.1% aa identity). The data suggest that genetic variation within the CAL viruses is less related to geographical distance than to similarity in ecological cycles.

The nucleotide sequence of the large (L) RNA segment of Dugbe (DUG) virus (Nairovirus, Bunyaviridae) was determined, completing the first entire genome sequence of a nairovirus. The L segment comprised 12255 nucleotides, making a total genome size of 18855 nucleotides, and the ends showed identity with the ends of the medium (M) and small (S) genomic segments. A single open reading frame (ORF) was present in the viral complementary strand, sufficient to encode a protein of 459 kDa. The predicted protein sequence showed the core polymerase motifs characteristic of the RNA-dependent RNA polymerases of segmented negative-stranded viruses. Comparison of the conserved motifs with the corresponding region of other segmented negative-strand viruses showed a closer relationship between nairoviruses and phleboviruses than with other Bunyaviridae or with other virus families. However, the core polymerase was the only function that could be assigned to a region of the DUG L gene.

Parvovirus B19 is the causative agent of a variety of clinical manifestations, ranging from asymptomatic to severe infection. The basis for this complex pattern of B19-associated diseases is as yet poorly understood. In general there are two different possibilities: firstly, the infected individuals may have a genetic or acquired predisposition, which renders them susceptible for a certain course of infection; secondly, differences in the B19 genome may result in different outcomes of infection. In order to investigate this second possibility we have partially sequenced the genomes of 20 different B19 isolates derived from serum samples from patients with various B19-associated diseases. Four distinct regions, which cover nearly half of the genome and include parts of the coding regions of all three major B19 proteins - NS1, VP1 and VP2, were selected for sequencing. Comparisons between the different extracted virus isolates at the DNA and protein levels revealed that isolates from patients with persistent parvovirus B19 infection show a tendency towards higher genome variability with respect to isolates derived from persons with acute infection.