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PubMedDate not supplied

Complexity and dynamics of HIV-1 quasispecies.

The human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins mediate virus entry into target cells by binding receptors of the cell membrane and fusing viral and cellular structures. In particular, recent crystallographic studies have clarified the complex role of the glycoprotein gp120 in the early phase of the infection. In this context the inter- and intra-host variability of the HIV-1 gp120 poses a major problem for the development of effective methods of immunization against this virus. In the present report, the relevant aspects emerging from the study of HIV-1 variability are addressed and several methodological approaches to evaluate HIV-1 diversity discussed.

Acquired Immunodeficiency Syndrome↗
PubMed1990

Alignment of U3 region sequences of mammalian type C viruses: identification of highly conserved motifs and implications for enhancer design.

We aligned published sequences for the U3 region of 35 type C mammalian retroviruses. The alignment reveals that certain sequence motifs within the U3 region are strikingly conserved. A number of these motifs correspond to previously identified sites. In particular, we found that the enhancer region of most of the viruses examined contains a binding site for leukemia virus factor b, a viral corelike element, the consensus motif for nuclear factor 1, and the glucocorticoid response element. Most viruses containing more than one copy of enhancer sequences include these binding sites in both copies of the repeat. We consider this set of binding sites to constitute a framework for the enhancers of this set of viruses. Other highly conserved motifs in the U3 region include the retrovirus inverted repeat sequence, a negative regulatory element, and the CCAAT and TATA boxes. In addition, we identified two novel motifs in the promoter region that were exceptionally highly conserved but have not been previously described.

Animals↗
PubMed1995

Molecular evolution of viruses: an interim summary.

The origin and molecular evolution of viruses in this issue is dealt with at two levels: (1) tracing the past evolutionary pathways of viruses belonging to RNA virus families, retroviruses, and small and large DNA viruses; (2) tracing current changes in the RNA and DNA viral genomes that lead to the evolution of new virus mutants. In this interim summary, a time scale for the evolutionary processes is given, based on the accumulated published knowledge concerning the postulated origins of life on planet Earth, and the hypothesis that living cells with RNA genomes may have emerged (the "RNA world hypothesis") that then developed into cells with DNA genomes in eukaryotic and prokaryotic cells (1-3). The ideas about the evolution of RNA and DNA viruses from ancient cellular RNA and DNA molecules over a period of 3.5 billion years are discussed. It may be possible that by studying virus genes and molecular processes in virus-infected cells, and their involvement in the shaping of the genomes of bacteria, yeast, plants, insects, mammals, and humans, it will be possible to understand the importance of viruses in past evolution and to predict their possible impact on current and future evolutionary trends in biology.

DNA, Viral↗
PubMed1996

[Evolution of canine parvovirus: loss and gain of the feline host].

Canine parvovirus is a newly emerged virus that was first isolated in 1978. As with all new viruses CPV continues to show active evolution, demonstrated by the appearance of new antigenic types. These new types termed CPV-2a and CPV-2b have replaced the original type CPV-2 throughout the world. The reason for the evolutionary advantage of the new viruses was most likely the acquisition of a new host, the cat. The new types are in contrast to CPV-2 able to infect and replicate in cats. Interestingly, about 10 per cent of the parvovirus isolates made from routine diagnostic cat materials were found to be canine parvovirus type 2a or 2b. The relevance of these findings for the epizootiology of parvovirus infection of dogs and cats and also for the vaccination are discussed.

Animals↗
PubMed2003

Newer viral encephalitides.

BACKGROUND: Viral encephalitis occurs in epidemic settings or is sporadic. New encephalitis patterns reflect the roles that biologic reservoirs and vectors play in determining virus-human interactions. "New" viral encephalitis can also result from human host modifications that increase susceptibility to neuroinvasive viral infection. REVIEW SUMMARY: Three human viruses, Nipah virus, Human Herpesvirus-6, and West Nile virus, present examples of how "new" viral encephalitides emerge in a specific geographic region or clinical setting. Nipah virus encephalitis emerged after the molecular evolution of a new zoonotic viral genus within the Paramyxovirinae family. Human herpesvirus-6 encephalitis has emerged in the immune suppressed human host harboring this ubiquitous but typically benign herpesvirus. West Nile virus encephalitis has emerged in the Western hemisphere after apparent abrupt translocation of this mosquito-borne virus to a distant geographic region with immunologically naive avian and human hosts. CONCLUSION: While the clinical features of these viral encephalitides are somewhat distinct, they each emerged as the result of human-derived factors that altered the biologic dynamic between humans and their viral pathogens.

Animals↗
PubMedDate not supplied

Multiple variants of HPV16 E6 gene in cervical invasive squamous cell carcinoma.

BACKGROUND: HPV16 is the most commonly detected genotype in cervical squamous cell carcinoma. E6 of HPV16 is a viral oncogene and has frequent DNA sequence variations whose encoded proteins have been shown to have heterogeneity in biochemical and biological properties. This study tried to establish whether the E6 variants derive from the infection pool or from spontaneous mutation in the host. MATERIALS AND METHODS: We combined the use of microdissection of multiple areas of tumor tissue, PCR-sequencing of HPV16 E6 and E5 genes and allele-specific amplification of PCR to analyze the E6 variations in four cases of cervical cancer (M4, M12, M13 and M23). RESULTS: We isolated two common (350G and 350T) and three rare (310G, 374T and 459C) E6 variations corresponding to five different E6 variants. The common E6 variations were always co-segregated with specific E5 variations. Both common variants persisted in all the four cases. Of three cases each had one additional rare E6 variant. CONCLUSION: The common E6 variants would derive from the infection pool, whereas the rare E6 variants may evolve from the mutation of either of the common E6 variants. This finding might have implications for the future study of natural HPV evolution, the design of viral vaccine and the carcinogenesis of cervical cancer.

Adult↗
PubMed2004

Accurate representation of the hepatitis C virus quasispecies in 5.2-kilobase amplicons.

Hepatitis C virus (HCV) exists as a swarm of genetically distinct but related variants, or a quasispecies, whose complexity and sequence evolution are critical to studies of viral pathogenesis. Because most studies of the HCV quasispecies have focused on a relatively small genomic segment, the first hypervariable region of the E2 gene, it is possible that viral complexity is occasionally underestimated (due to primer mismatch) and that sequence evolution is misperceived due to unrecognized covariation. This report describes a sensitive and reproducible method to amplify most of the HCV genome as a single 5.2-kb amplicon by using primers directed at relatively conserved genomic segments. Using 52 specimens obtained during acute infection over a range of viral RNA concentrations, the overall rate of successful amplification was 94% and varied in a concentration-dependent manner, with successful amplification in 26 of 26 (100%) specimens at greater than 10(5) IU/ml, 15 of 16 (94%) at 10(4) to 10(5) IU/ml, 6 of 7 (86%) at 10(3) to 10(4) IU/ml, and 2 of 3 (67%) at less than 10(3) IU/ml. Quasispecies complexity, determined by using this novel long-amplicon method followed by heteroduplex mobility assay combined with single-stranded conformational polymorphism (HDA+SSCP) analysis, was very high, even during acute HCV infection, when 10 to 21 (median, 16) different HDA+SSCP patterns were detected among 33 cDNA clones examined. Replicate analyses indicate that this diversity is not dominated by random errors generated during amplification. Therefore, the HCV quasispecies is highly complex even during acute infection and is accurately represented in amplicons representing more than half of the viral genome.

Amino Acid Sequence↗
PubMed1989

Natural history of woodchuck hepatitis virus infections during the course of experimental viral infection: molecular virologic features of the liver and lymphoid tissues.

In this study, the kinetic patterns of woodchuck hepatitis virus (WHV) infection were monitored in the liver and the five primary components of the lymphoid system (peripheral blood lymphocytes, lymph nodes, bone marrow, spleen, and thymus). Groups of woodchucks experimentally infected with a standardized inoculum of WHV were sacrificed at different times over a 65-week period beginning in the preacute phase of viral infection and continuing to the period of serologic recovery or the establishment of chronic infections and subsequent hepatocellular carcinoma. Infection by WHV was not limited to the liver but involved the major components of the lymphoid system during all stages of virus infection. A complex series of kinetic patterns was observed for the appearance of WHV DNA in the different lymphoid compartments and the liver during the entire course of viral infection. A progressive evolution of different WHV genomic forms related to the replicative state of WHV was also observed. Lymphoid cells of the bone marrow were the first cells in which WHV DNA was detected, followed in order by the liver, the spleen, peripheral blood lymphocytes, lymph nodes, and finally the thymus. Several differences were observed in the cellular WHV DNA patterns between woodchucks that developed chronic WHV infections and those that serologically recovered from acute WHV infections. The observations compiled in this study indicate that the host lymphoid system is intimately involved in the natural history of hepadnavirus infections from the earliest stages of virus entry.

Animals↗
PubMed2003

Correlation of sICAM-1 and sVCAM-1 level with biochemical, histological and viral findings in chronic hepatitis C after interferon-alpha + ribavirin therapy.

UNLABELLED: Intercellular cell adhesion molecules-1 (ICAM-1) and vascular cell adhesion molecules-1 (VCAM-1) are expressed in a high quantity on hepatocytes and at the level of endothelium cells from sinusoidal vessels in the liver tissue of patients with chronic hepatitis C. The soluble forms of these molecules sICAM-1 and sVCAM-1 can be determined in the serum of patients through the immunoenzymatic technique (ELISA). THE AIM: of the study was to analyse the base level of these molecules and the changes induced through the combined treatment of interferon-alpha (IFN- alpha) and ribavirin (Rib). MATERIALS AND METHODS: Twenty patients suffering from viral chronic hepatitis C were studied: 10 patients responded completely to antiviral treatment and 10 patients showed no response at the end of the treatment. At the end of the therapy patients were placed under biochemical observation for a further six months. The serum concentration of sICAM-1 and sVCAM-1 was measured using ELISA assay at the beginning and the end of the combined treatment: six months IFN 3MU (three times a week) associated with Rib. RESULTS: Statistically, a significant correlation was observed between the values of sICAM-1 pretreatment and the level of viremia, gamma glutamiltrans-peptidase (GGT), but without correlation to the alanin amino transferase (ALT) level. The value of sICAM-1 was significantly higher in patients who had fibrosis score F: 3-4. After the treatment, the serum concentration of sICAM-1 dropped significantly in patients with sustained biochemical response in comparison to patients who had an unsustained response or had no response whatsoever. A significant correlation between the sVCAM-1 pre-treatment value and the level of viremia, GGT, ALT was not established. CONCLUSIONS: The level of sICAM-1 could be a useful parameter in the observation of the disease evolution of patients with viral chronic hepatitis C treated with IFN-alpha and Rib.

Adult↗
PubMed1992

SIV from stump-tailed macaques: molecular characterization of a highly transmissible primate lentivirus.

Over the past 6 years, simian immunodeficiency viruses (SIVs) have been isolated from four distinct species of macaques (Macaca mulatta, M. fascicularis, M. nemestrina, and M. arctoides) in captivity in the United States. However, the epidemiologic and genetic relationships among SIVs from the four species are not well understood. SIV from stump-tailed macaques (M. arctoides) (SIVstm) is unusual in that it has been associated with outbreaks of infection characterized by aggressive spread within stump-tailed macaque colonies at two separate primate centers in the United States. To characterize SIVstm at the molecular level, we have derived six biologically active viral DNA clones by polymerase chain reaction amplification of genomic DNA from infected cells. Nucleotide sequence analyses of one clone (SIVstm/37.16) showed that SIVstm was indeed a member of the previously defined group of simian lentiviruses that are closely related to the human immunodeficiency virus type 2 (HIV-2). However, our data indicate that SIVstm is equidistantly related to the other SIVs from macaques (SIVmac 251/142 and SIVmne) and SIV from African sooty mangabeys (SIVsmm). These findings suggest that SIV from captive macaques may have originated from several cross-species transmissions from imported sooty mangabeys and that additional spread has been fostered by the exchange of macaques among primate centers.

Amino Acid Sequence↗
PubMed1989

Scrambled duplications in the feline leukemia virus gag gene: a putative pattern for molecular evolution.

The present study is a detailed computer-assisted analysis of the feline leukemia virus gag gene nucleotide sequence together with its flanking sequences (ST-FeLV GAG) that is compared with the aligned sectors of the Moloney strain of murine leukemia virus (Mo-MuLV GAG) and of three strains of feline sarcoma virus. It shows that perfectly matched repeated oligomers up to 13 nucleotides long are overrepresented and scattered throughout both ST-FeLV GAG and Mo-MuLV GAG, in noncoding and coding sectors, with no stringent correlation to codon usage in ST-FeLV gPr80gag. Many repeated oligomers share a core consensus that is intriguingly part of the inverted repeat at the termini of the long terminal repeat. Local scrambled repetitions of nucleotide subsequences have been found; they suggest a model of molecular evolution by slippage-like mechanisms. Thus, viral genomes could be subject to the same evolutionary mechanisms that are now known to be operating extensively in eukaryotic genomes. The data are discussed in light of putative patterns of molecular evolution.

Antigens, Viral↗
PubMed1984

Segmental homology and internal repetitiousness identified in putative nucleic acid polymerase and human hepatitis B surface antigen of human hepatitis B virus.

In a previous paper, it was argued that only those coding sequences descended from oligomeric repeats (the number of bases in the oligomeric unit not being a multiple of 3) can retain sufficiently long alternative open reading frames, and that such alternative open reading frames serve as the reservoir for the sudden generation of new polypeptide chains with novel functions. It was suggested that plasmid-encoded 6-amino hexanoic acid linear oligomer hydrolase that suddenly endowed Flavobacterium sp. K172 with the capacity to live off nylon by-products arose by the above mechanism. A corollary to the above argument is the expectation that those viral base sequences that are known to use two of the three alternative reading frames to encode two different polypeptide chains should invariably contain recognizable remains of the oligomeric tandem repeats, and as a consequence, various oligopeptidic repeats should also be present in the amino acid sequence of each. Furthermore, two polypeptide chains encoded by the same base sequence translated in different reading frames should show segmental homology of the type depicted previously. In the present paper, the base sequence of human hepatitis B virus ayw subtype that encodes an 832 amino acid residue long putative nucleic acid polymerase in one reading frame and a 226 residue long human hepatitis B surface antigen in the other reading frame was examined. All three predictions noted above were satisfied.

Amino Acid Sequence↗
PubMed2026

A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas.

CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) systems consisting of a Vipr protein ancestral to the earliest CRISPR-Cas effectors and VIPR RNAs (vrRNAs) comprising alternating GGY/NN motifs. Unlike canonical guide RNAs that pair with target nucleic acids through contiguous complementarity, vrRNAs recognize double-stranded DNA through a noncontiguous code in which the variable NN dinucleotides collectively specify a gapped target sequence. Natural vrRNA targets suggest that VIPR systems act against competing phages, and we demonstrate programmable phage defense by redirecting the complex for transcriptional repression. These results suggest that adaptive immunity originated from ancient warfare between viruses, revealing a previously unidentified logic for encoding information in sequence.

CRISPR-Cas Systems↗
PubMed1992

Low degree of human T-cell leukemia/lymphoma virus type I genetic drift in vivo as a means of monitoring viral transmission and movement of ancient human populations.

We have studied the genetic variation of human T-cell leukemia/lymphoma virus type I (HTLV-I) isolates in the same individuals over time, as well as of HTLV-I isolates from various parts of the world. The viral DNA fragment studied encodes the carboxy terminus of gp46 and almost all of gp21, both of which are envelope glycoproteins. Samples were obtained from native inhabitants of five African countries, two South American countries, China, the French West Indies, and Haiti and included 14 patients with tropical spastic paraparesis/HTLV-I-associated myelopathy, 10 patients with adult T-cell leukemia, 1 patient with T-cell non-Hodgkin's lymphoma, and 3 healthy HTLV-I-seropositive individuals. DNA analyses of HTLV-I sequences demonstrated that (i) little or no genetic variation occurred in vivo in the same individual or in different hosts from the same region carrying the same virus, regardless of their clinical statuses; (ii) changes in nucleotide sequences in some regions of the HTLV-I genome were diagnostic of the geographical origin of the viruses; (iii) HTLV-I sequences from West African countries (Mauritania and Guinea Bissau) and some from the Ivory Coast and Central African Republic were virtually identical to those from the French West Indies, Haiti, French Guyana, and Peru, strongly suggesting that at least some HTLV-I strains were introduced into the New World through infected individuals during the slave trade events; and (iv) the Zairian HTLV-I isolates represent a separate HTLV-I cluster, in which intrastrain variability was also observed, and are more divergent from the other HTLV-I isolates. Because of the low genetic variability of HTLV-I in vivo, the study of the proviral DNA sequence in selected populations of infected individuals will increase our knowledge of the origin and evolution of HTLV-I and might be useful in anthropological studies.

Base Sequence↗
PubMed1994

Sequence diversity within the reovirus S2 gene: reovirus genes reassort in nature, and their termini are predicted to form a panhandle motif.

To better understand genetic diversity within mammalian reoviruses, we determined S2 nucleotide and deduced sigma 2 amino acid sequences of nine reovirus strains and compared these sequences with those of prototype strains of the three reovirus serotypes. The S2 gene and sigma 2 protein are highly conserved among the four type 1, one type 2, and seven type 3 strains studied. Phylogenetic analyses based on S2 nucleotide sequences of the 12 reovirus strains indicate that diversity within the S2 gene is independent of viral serotype. Additionally, we found marked topological differences between phylogenetic trees generated from S1 and S2 gene nucleotide sequences of the seven type 3 strains. These results demonstrate that reovirus S1 and S2 genes have distinct evolutionary histories, thus providing phylogenetic evidence for lateral transfer of reovirus genes in nature. When variability among the 12 sigma 2-encoding S2 nucleotide sequences was analyzed at synonymous positions, we found that approximately 60 nucleotides at the 5' terminus and 30 nucleotides at the 3' terminus were markedly conserved in comparison with other sigma 2-encoding regions of S2. Predictions of RNA secondary structures indicate that the more conserved S2 sequences participate in the formation of an extended region of duplex RNA interrupted by a pair of stem-loops. Among the 12 deduced sigma 2 amino acid sequences examined, substitutions were observed at only 11% of amino acid positions. This finding suggests that constraints on the structure or function of sigma 2, perhaps in part because of its location in the virion core, have limited sequence diversity within this protein.

Amino Acid Sequence↗
PubMed2006

Continuing evolution of H9 influenza viruses in Korean poultry.

We analyzed the evolution of H9 influenza viruses isolated from Korean chicken farms from 2002 to 2004. Korean H9 viruses formed two antigenically distinct groups: those isolated from 1996 to mid-2003, and those isolated from late 2003 through 2004. Most of the 2004 isolates showed greater cross-reactivity with the second group than with the first group. Phylogenetic analysis of the 12 viruses studied revealed three genotypes of H9N2 viruses and showed that reassortment had occurred. One isolate, Ck/Kor/164/04, belonged to the H9N8 subtype. Its HA and PB1 genes were similar to those of the H9N2 viruses, but its other genes were closely related to H3N8 viruses. This report is the first (to our knowledge) of H9N8 infection in this host. The pathogenicity of the early isolates altered due to antigenic drift and reassortment, leading to H9 avian influenza viruses in Korea that potentially can expand their host range to mammalians.

Animals↗
PubMed2003

Evolution of North American PVY(NTN) strain Tu 660 from local PVY(N) by mutation rather than recombination.

A North American (NA) isolate of tobacco veinal necrotic strain of Potato virus Y (PVY(N)) (N-Jg) and a NA isolate of potato tuber necrotic strain of Potato virus Y (PVY(NTN) (Tu 660) were tested for their phenotypes by inoculation to potato plants of three potato cultivars. Upon inoculation with Tu 660, tubers of the cultivars 'Norchip' and 'Ranger Russet' developed potato tuber necrotic ringspot disease (PTNRD) but not the tubers of 'Russet Burbank'. N-Jg failed to induce PTNRD in the tested cultivars. The genomic RNAs of both strains were completely sequenced and analysed. High homology (98% and 99% identity on nucleotide and polyprotein, respectively) was found between Tu 660 and N-Jg. When polyproteins were compared with other isolates, high identity was observed between Tu 660 and an European (Eu) PVY(N)-605 (98%) and with an Eu-PVY(NTN)-H (96%). However, when individual mature proteins were compared, much lower identities (86.5-94%) were found between Tu 660 and PVY9(NTN))-H compared to 98-99.5% between Tu 660 and PVY(N)-605 in the P3, 6K1 and CI regions. Further sequence analysis indicated that the PVY(NTN)-H is a hybrid molecule of the genomic RNA recombination of PVY(O) and Eu-PVY(N) as shown by Glais et al. (Arch Virol 147, 363-378), whereas NA-PVY(NTN) Tu 660 is free of recombination points. Phylogenetic analysis confirmed this observation, and suggested that, in light of high homology, the Tu 660 might have evolved from NA-PVY(N) by mutations rather than the genome recombinations. The non-recombinant nature of NA-PVY(NTN) Tu 660 strongly suggests that the recombinant structure of genome is not a necessary prerequisite for the PTNRD phenotype.

Cloning, Molecular↗
PubMed1987

Mechanisms of liver cell damage in acute hepatitis B.

Markers of hepatitis B viral infection and the evolution of immune response to these were compared with serum alanine aminotransferase (ALT) levels in adult male and non-pregnant and pregnant female patients with acute hepatitis B from the time of onset of disease to the seventh week. In the adult male and non-pregnant female patients, the peak ALT levels of about 360 IU/litre, seen at the time of onset, gradually declined during the course of the disease. Significantly, even in the seventh week, the median ALT level was abnormal (80 IU/litre). In contrast, the disease was mild in pregnant patients and the ALT levels declined rapidly, returning to normal by the third week. Markers associated with HBV replication, i.e., serum HBV-DNA and HBeAg, declined early in the course of the disease in both groups. The anti-HBc-IgM and anti-HBe responses were well evolved early in the course of the disease in both groups. HBsAg was present in the serum in large amounts (1-1.5 X 10(4) AU/100 microliter) early in the course of the disease and remained so up to the seventh week. Even the pregnant patients who had recovered clinically by the fourth week continued to have HBsAg in their sera in large amounts in spite of normal ALT levels. LMI and LTT responses to HBsAg, which were practically absent in the first week, gradually increased to a peak during the fourth week and remained elevated up to the seventh week in adult male and non-pregnant female patients. In contrast, LMI response to HBsAg was absent in pregnant patients with acute hepatitis B even up to the fourth week Thus, continued liver cell necrosis after the fourth week, as indicated by raised ALT levels, may be associated with T cell responses to HBsAg.

Acute Disease↗