Evolutionary relationships between papovaviruses and their hosts

The papovaviridae family consists of two genera, the papillomaviruses (PV) and the polyomaviruses (Py-V). Both genera are distinguished by morphological (larger sizes of the PV) and several biological characteristics. The genomes of either of the two genera share highly conserved DNA regions and a common antigenic determinant, located in their major capsid polypeptides. On the basis of these data an evolutionary relationship among the members of PV and Py-V, respectively, has been suggested. No homology has been found for either DNA- or protein sequences between PV and Py-V and the question of a common ancestor for both viral genera remains open. We have started to characterize the genome of a papilloma producing papovavirus of the Syrian hamster (HaPV). Most of the known biological characteristics of the HaPV suggest it should be classified as a papilloma-like virus. However, the molecular weight of about 3.5 X 10(6) daltons found for the circular duplex DNA lies within the range given for SV 40 and polyoma virus (Py). Analysis of the HaPV genome by cleavage with 21 different restriction endonucleases, location of specific binding sites of phage T 4 gene 32 protein and E. coli RNA polymerase on the viral DNA demonstrated that the HaPV differed distinctly from all other currently known papovaviruses. The HaPV genome was also analyzed by filter hybridization and electron microscopy under conditions of varied stringency for nucleotide sequence homology with the genomes of different papovaviruses of both genera. Whereas no homologous DNA regions could be found between the genomes of HaPV and the human PV types 1 and 4, only under nonstringent conditions (Tm-43 degrees C) stable hybrids were formed between HaPV-, SV 40- and the DNA of a PV isolated from Mastomys natalensis (MnPV). On the other hand extensive homology was detected between the genomes of HaPV and Py even under stringent hybridization conditions (Tm-28 degrees C). The homologous DNA segments mapped on the Py and partially on the SV 40 genome were found to be the most strongly conserved DNA regions among the Py-V genus. These results are discussed with respect to a classification of the HaPV within the papovaviridae family.     

Structure of the long terminal repeat of simian lymphotropic virus type III (African green monkey) and its relatedness to that of HIV

The simian T-lymphotropic virus type III (STLV-III[AGM]) is a retrovirus in wild African green monkeys which is serologically related to the human T-lymphotropic virus type III (HTLV-III/LAV-1/HIV) and other related human retroviruses. The long terminal repeats (LTR) contained in clones of viral DNA of (STLV-III[AGM]) were subcloned in M13 and their DNA sequence was determined and compared with that of HIV (HTLV-III[BH10]). The STLV-III(AGM) LTR is considerably larger than that of HTLV-III(BH10) (800 bp vs 634 bp) and contains a 498 bp U3 region, a 176 bp R region, and a 126 bp U5 region. These two LTR sequences share regions of significant homology. Regions of greatest homology include the 5' portion of U3, a core enhancer sequence in U3, sequences including and surrounding the TATAA promoter box in U3 and the AATAAA polyadenylation/termination signal in R, and the 3'-most region of U5. The relatively larger size of the STLV-III LTR is due to the presence in all three parts of the LTR of sequences which have no apparent homolog in the HIV LTR. Overall, the two LTRs are 47% homologous. Even greater homology (75%) is evident with a 300 bp segment including R and some of U3 from the LTR of another human retrovirus, HIV-2/LAV-2. The STLV-III LTR contains an imperfect 28 bp direct repeat in the R region which is not present in HIV. There are no obvious direct repeats in U3 homologous to the 10 bp repeat in the U3 of HTLV-III.(ABSTRACT TRUNCATED AT 250 WORDS)     

Retroviral protease-like gene in the vaccinia virus genome.

The retroviral protease-encoding region, PR, situated between the gag and pol genes, underwent gene duplication in the lineage now represented by simian retrovirus type 1; the sequence of the duplicated segment has diverged considerably from the present PR sequence [Power, M.D., Marx, P.A., Bryant, M.L., Gardner, M.B., Barr, P.J. & Luciw, P.A. (1986) Science 231, 1567-1572]. The PR-like duplicated gene segment was at some point translocated to a new site within the pol gene of a lentivirus (subsequent to the divergence of human immunodeficiency virus type 1), where it has been maintained. We have identified in the vaccinia virus genome a sequence that is homologous to the PR-like duplicated gene segment of both types of retrovirus in an open reading frame whose product is predicted to be a 16.2-kDa protein. The vaccinia PR-like gene is located in the HindIII F fragment, and its product displays 31-34% amino acid identity to the two types of retroviral duplicated protease sequences over a region encompassing 125 amino acid residues. Sequences flanking the vaccinia gene showed no significant homology at either the DNA or amino acid level to the retroviruses. Nuclease S1 and primer extension analyses determined that the vaccinia gene is transcribed early in infection.     

Genetic organization and diversity of the hepatitis C virus.

The nucleotide sequence of the RNA genome of the human hepatitis C virus (HCV) has been determined from overlapping cDNA clones. The sequence (9379 nucleotides) has a single large open reading frame that could encode a viral polyprotein precursor of 3011 amino acids. While there as little overall amino acid and nucleotide sequence homology with other viruses, the 5' HCV nucleotide sequence upstream of this large open reading frame has substantial similarity to the 5' termini of pestiviral genomes. The polyprotein also has significant sequence similarity to helicases encoded by animal pestiviruses, plant potyviruses, and human flaviviruses, and it contains sequence motifs widely conserved among viral replicases and trypsin-like proteases. A basic, presumed nucleocapsid domain is located at the N terminus upstream of a region containing numerous potential N-linked glycosylation sites. These HCV domains are located in the same relative position as observed in the pestiviruses and flaviviruses and the hydrophobic profiles of all three viral polyproteins are similar. These combined data indicate that HCV is an unusual virus that is most related to the pestiviruses. Significant genome diversity is apparent within the putative 5' structural gene region of different HCV isolates, suggesting the presence of closely related but distinct viral genotypes.     

Cloning of the cellular receptor for amphotropic murine retroviruses reveals homology to that for gibbon ape leukemia virus.

The host and tissue specificity of retrovirus infection is largely determined by specific cellular receptors that mediate virus entry. Genes encoding these receptors are widely distributed in the genome, and the receptors identified to date show no sequence similarity. We have identified the cellular receptor for amphotropic murine retroviruses, Ram-1, by screening a rat cDNA expression library introduced into amphotropic virus-resistant hamster cells. The 656-amino acid receptor is homologous to the gibbon ape leukemia virus receptor at both hydrophobic termini but is highly divergent in the central hydrophilic region. Both receptors appear to be integral membrane proteins having multiple membrane-spanning regions. Identification of this family of receptors will help define the evolutionary relationship between retroviruses and their cellular receptors.     

Identification of a poxvirus gene encoding a uracil DNA glycosylase.

An open reading frame, BamHI D6R, from the central highly conserved region of the Shope fibroma virus (SFV) genome was sequenced and found to have significant homology to that of uracil DNA glycosylases from a number of organisms. Uracil DNA glycosylase catalyzes the initial step in the repair pathway that removes potentially mutagenic uracil from duplex DNA. The D6R polypeptide was expressed in reticulocyte lysates programmed with RNA transcribed from an expression vector containing the T7 RNA polymerase promoter. A highly specific ethidium bromide fluorescence assay of the in vitro translation product determined that the encoded protein does indeed possess uracil DNA glycosylase activity. Open reading frames from other poxviruses, including vaccinia virus (HindIII D4R) and fowlpox (D4), are highly homologous to D6R of SFV and are predicted to encode uracil DNA glycosylases. Identification of the SFV uracil DNA glycosylase provides evidence that this poxviral protein is involved in the repair of the viral DNA genome. Since this enzyme performs only the initial step required for the removal of uracil from DNA, creating an apyrimidinic site, we suggest that other, possibly virus-encoded, repair activities must be present in the cytoplasm of infected cells to complete the uracil excision repair pathway.     

乙型肝炎病毒表达载体pHY106在筛选抗病毒药物中的意义

目的应用新的HBV表达载体,建立体外筛选临床抗HBV药物的方法。方法克隆对拉米夫定耐药的CHB患者体内HBV全基因组,然后将其亚克隆到HBV真核表达载体pHY106,体外转染Huh7细胞,检测转染后不同时间HBsAg、HBeAg、HBV DNA及HBV复制中间体水平。分析拉米夫定和阿德福韦对HBV基因表达和复制的抑制作用,指导临床用药。结果成功构建全部8个HBV临床分离株全基因组真核表达质粒,HBV聚合酶基因YMDD有5个产生YVDD突变,3个产生YIDD突变。该质粒上HBV基因能在Huh7细胞中进行复制和表达,拉米夫定不能体外抑制HBV复制,阿德福韦抑制了HBV在Huh7细胞中的复制,抑制程度与药物浓度相关。阿德福韦在患者体内也抑制了HBV的复制。结论新建立的体外筛选抗HBV药物的方法能用于临床快速筛选抗HBV药物,对CHB的治疗用药具有指导意义。     

Molecular cloning and partial characterization of unintegrated linear DNA from gibbon ape leukemia virus.

We have cloned the complete genome of an oncogenic primate retrovirus, the San Francisco isolate of gibbon ape leukemia virus, in a lambda phage vector. DNA sequence analysis and restriction endonuclease mapping of the inserted linear provirus demonstrated 9-base pair inverted repeats at its ends, flanking direct terminal repeats 470 base pairs in length. The (-) strong stop region of this DNA showed surprisingly low sequence homology to that of another gibbon ape leukemia virus isolate from an animal with similar disease. Analysis of the clone also revealed the terminal phosphate configuration of the linear provirus. The recombinant phage is suitable for direct use as a hybridization probe to detect homologous retroviral sequences in human cell lines.     

Evidence against a requisite role for defective virus in the establishment of persistent hepadnavirus infections.

The factors involved in the establishment of persistent hepadnavirus infection are poorly understood. Recent findings demonstrate that the sequence of the genome of hepatitis B virus (HBV) is variable in infected individuals and that, in some cases, virus mutants predominate. Our objectives in the present study were to analyze the variability of woodchuck hepatitis virus (WHV) genomes in an infected animal and to determine whether sequence heterogeneity played a critical role in the ability of WHV to induce chronic infection. We cloned and determined the complete nucleotide sequence of three supercoiled genomes from an animal that became infected after inoculation with a standardized WHV serum pool (i.e., the WHV7 virus pool). We found that there were four nucleotide substitutions among the three genome sequences as well as a 73-nucleotide deletion in one of the recombinants. DNA transfection experiments revealed that only one of the three recombinants was capable of independent replication. These data suggest that a significant proportion of replicative templates in woodchucks that are infected with WHV are defective virus genomes. Next, we compared the outcome of acute infection after inoculation with a serum pool containing a uniform population of replication competent virus (i.e., the WHV7R pool) with a serum pool composed of WHV genomes of variable sequence. The WHV7R serum pool originated from a woodchuck that became a chronic carrier after in vivo transfection of the liver with the infectious WHV7 recombinant. Neonatal woodchucks were inoculated with 5 x 10(6) WHV genome equivalents of either the WHV7 pool or the WHV7R pool. All animals in the study became acutely infected with WHV. Of the animals infected with the WHV7 serum pool, 65% became chronic carriers, while 80% of the animals infected with the WHV7R serum pool developed chronic infection. Thus, infection of woodchucks with a serum pool containing defective virus resulted in a rate of chronic WHV infection that was similar to, or even lower than, a rate from a pool containing only wild-type virus. This suggests that the presence of defective virus in the inoculum is not a prerequisite for the establishment of persistent hepadnavirus infections.     

Conserved cysteine and histidine residues of the avian myeloblastosis virus nucleocapsid protein are essential for viral replication but are not "zinc-binding fingers"

The nucleocapsid protein from the Rous sarcoma virus has two regions of sequence with the motif Cys-Xaa-Xaa-Cys-Xaa-Xaa-Xaa-Gly-His-Xaa-Xaa-Xaa-Cys. All retrovirus nucleocapsid proteins contain one or two of these motifs, and they represent the only conserved sequences among these proteins. Sequence analysis of nucleocapsid from avian myeloblastosis virus shows that it also contains two Cys-His sequences and, in fact, differs from the Rous sarcoma nucleocapsid protein only in three residues near the carboxyl terminus. The hypothesized role of the conserved cysteines and histidines as zinc ligands was tested experimentally. No tightly bound metal ions were detected for avian myeloblastosis nucleocapsid protein, and the molar amount of zinc in virions was less by a factor of 50 than that of the nucleocapsid protein. Added Zn2+ did not significantly affect nucleocapsid binding to poly(ethenoadenylic acid) or its secondary structure, as determined from circular dichroism. Nevertheless, the conserved cysteine and histidine residues of the Rous sarcoma (Prague-C strain) nucleocapsid protein are essential for fully functional virus, as shown by the fact that single-site substitutions of five of the six conserved cysteines and either of the two histidine residues blocked viral replication.     

不同疟区恶性疟原虫地理株谷氨酸富有蛋白基因R2区序列分析及分型

[目的 ]测定云南与海南两省不同疟区恶性疟原虫分离株谷氨酸富有蛋白 (GLURP)基因的部分序列及了解其分型。[方法 ]采用套式PCR方法特异性扩增GLURP基因R2区片段 ,并将该基因片段克隆于T载体 ,用双脱氧末端终止法测定不同长度的阳性克隆核苷酸序列 ,并应用DNAStar软件对云南与海南两省分离株GLURP基因及蛋白序列进行比较和分析。[结果 ]首次发现云南与海南两省恶性疟原虫至少存有 7个大小不同的GLURP等位基因型虫株 ,其基因片段变化范围为 6 0 0～ 15 0 0bp。不同分离株的GLURP基因R2区具高度保守性 ,其由编码 19～ 2 0个氨基酸的碱基的基本重复单位构成 ,该基因具有长度的多态性 ,表现在碱基基本重复单位的数目不同。序列分析结果表明 ,我国不同分离株之间或同一地区不同株之间GLURP基因及氨基酸序列具有高度的同源性 ,无明显的地理差异。 [结论 ]不同分离株GLURP基因结构的高度保守性及碱基重复片段数目的多态性 ,对研究疫苗候选抗原和建立疟原虫基因分型方法具有一定理论价值。     

A new endogenous primate type C virus isolated from the Old World monkey Colobus polykomos.

A new, genetically transmitted retrovirus has been isolated from the Old World monkey Colobus polykomos. This virus, designated CPC-1, is readily transmitted to both feline and human cells in culture. Nucleic acid hybridization studies reveal that there are 50-70 copies of the CPC-1 genome in colobus cellular DNA. Related virogene sequences can be detected in the DNA of all other Old World monkeys, as well as in the DNA of at least one ape species, the chimpanzee, indicating that this virus has been genetically transmitted in primates for 30-40 million years. CPC-1 is partially related to the type C virus previously isolated from stumptail monkeys (MAC-1). These two viruses have nucleic acid sequence homology, antigenic crossreactivity in their major viral structural protein, and a very similar host range in vitro. CPC-1 and MAC-1 therefore belong to the same class of genetically transmitted primate type C viruses and, as such, represent the first example in primates of analogous endogenous retroviruses isolated from two distantly related species.     

Giardiavirus double-stranded RNA genome encodes a capsid polypeptide and a gag-pol-like fusion protein by a translation frameshift.

Giardiavirus is a small, nonenveloped virus comprising a monopartite double-stranded RNA genome, a major protein of 100 kDa, and a less abundant polypeptide of 190 kDa. It can be isolated from the culture supernatant of Giardia lamblia, a parasitic flagellate in human and other mammals, and efficiently infects other virus-free G. lamblia. A single-stranded copy of the viral RNA can be electroporated into uninfected G. lamblia cells to complete the viral replication cycle. Giardiavirus genomic cDNA of 6100 nt was constructed and its sequence revealed the presence of two large open reading frames that are separated by a -1 frameshift and share an overlap of 220 nt. The 3' open reading frame contains all consensus RNA-dependent RNA polymerase sequence motifs. A heptamer-pseudoknot structure similar to those found at ribosomal slippage sites in retroviruses and yeast killer virus was identified within this overlap. Immunostudies using antisera against synthesized peptides from four regions in the two open reading frames indicated that the 100- and 190-kDa viral proteins share a common domain in the amino-terminal region. But the 190-kDa protein makes a -1 switch of its reading frame beyond the presumed slippage heptamer and is therefore a -1 frameshift fusion protein similar to the gag-pol fusion protein found in retroviruses.     

A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2

Sequence analysis of a 10-kb region of the genome of the marine cyanomyovirus S-PM2 reveals a homology to coliphage T4 that extends as a contiguous block from gene (g)18 to g23. The order of the S-PM2 genes in this region is similar to that of T4, but there are insertions and deletions of small ORFs of unknown function. In T4, g18 codes for the tail sheath, g19, the tail tube, g20, the head portal protein, g21, the prohead core protein, g22, a scaffolding protein, and g23, the major capsid protein. Thus, the entire module that determines the structural components of the phage head and contractile tail is conserved between T4 and this cyanophage. The significant differences in the morphology of these phages must reflect the considerable divergence of the amino acid sequence of their homologous virion proteins, which uniformly exceeds 50%. We suggest that their enormous diversity in the sea could be a result of genetic shuffling between disparate phages mediated by such commonly shared modules. These conserved sequences could facilitate genetic exchange by providing partially homologous substrates for recombination between otherwise divergent phage genomes. Such a mechanism would thus expand the pool of phage genes accessible by recombination to all those phages that share common modules.     

Evidence of transmission of hepatitis B virus to spouses from sequence analysis of the viral genome

Heterosexual contact is one of the common routes of transmission for hepatitis B virus (HBV) among adults in Taiwan, but only a few studies have provided direct evidence at the level of the HBV genome of infected couples with acute non-fulminant hepatitis to document a common source. By cloning and sequencing polymerase chain reaction-amplified HBV-DNA, we analysed the sequences of the conserved region of the surface gene (nucleotide (nt) 305–513, representing 6.5% of the viral genome) of HBV in five HBV-infected index patients, their spouses and four randomly selected HBV carriers as controls. Risk factors associated with acute HBV infection in index cases were sexual contact with their spouses within 3 months before the onset of hepatitis. For all five couples, the HBV-infected index patient and the spouse shared a 100% sequence homology of HBV-DNA. In contrast, there was significantly more variation (mean heterogeneity 6.1%, range 1–13.9%) in the amplified region between the five couples and between each couple and the controls ( P < 0.001). This study demonstrated that sequence analyses can correlate well with epidemiological findings and confirm the value of the molecular approach for linked infections of HBV through heterosexual contact between spouses. Susceptible adults should receive vaccination.