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PubMed2004

Sequence evolution of putative cytotoxic T cell epitopes in NS3 region of hepatitis C virus.

AIM: Quasispecies of hepatitis C virus (HCV) are the foundation for rapid sequence evolution of HCV to evade immune surveillance of hosts. The consensus sequence evolution of a segment of HCV NS3 region, which encompasses putative cytotoxic T cell epitopes, was evaluated. METHODS: Three male patients, infected with HCV through multiple transfusions, were identified from clinical symptoms and monitored by aminotransferase for 60 months. Blood samples taken at months 0, 32, and 60 were used for viral RNA extraction. A segment of HCV NS3 region was amplified from the RNA extraction by RT-PCR and subjected to subcloning and sequencing. HLA types of these three patients were determined using complement-dependent microlymphocytotoxic assay. CTL epitopes were predicted using MHC binding motifs. RESULTS: No patient had clinical symptoms or elevation of aspartate/alanine aminotransferase. Two patients showed positive HCV PCR results at all 3 time points. The other one showed a positive HCV PCR result only at month 0. A reported HLA-A2-restricted CTL epitope had no alteration in the HLA-A2-negative carrier over 60 months. In the HLA-A2-positive individuals, all the sequences from 0 month 0 showed an amber mutation on the initial codon of the epitope. Most changes of consensus sequences in the same patient occurred on predicted cytotoxic T cell epitopes. CONCLUSION: Amber mutation and changes of consensus sequence in HCV NS3 region may be related to viral immune escape.

Adult↗
PubMed1992

Evolution of the fusion protein gene of human parainfluenza virus 3.

The nucleotide sequences of the fusion (F) gene of 15 clinical strains of human parainfluenza virus 3 (HPIV3) isolated between 1959 and 1987 were compared with the F gene sequence of the prototype strain, Wash/47885/57. Nucleotide sequence diversity was greatest in the noncoding regions of the F gene; however, regions believed to function as transcriptional signals were completely conserved. Amino acid sequences were highly conserved and all but a few amino acid substitutions were conservative in nature. Sequence comparisons indicate heterogeneity in HPIV3 F genes; however, a significant proportion of nucleotide changes are maintained after they first appear and seem to be accumulating with time. Phylogenetic analysis suggests that there are 2 lineages of HPIV3 in North America. The two lineages can be distinguished by specific amino acid differences in the F protein, which correlate with differences in antigenic properties and neutralization patterns of HPIV3. The pattern of HPIV3 evolution, based on the analysis of F gene sequences, most closely resembles that of influenza virus B, vesicular stomatitis virus and Newcastle disease virus.

Amino Acid Sequence↗
PubMed2006

The origin of viruses and their possible roles in major evolutionary transitions.

Viruses infecting cells from the three domains of life, Archaea, Bacteria and Eukarya, share homologous features, suggesting that viruses originated very early in the evolution of life. The three current hypotheses for virus origin, e.g. the virus first, the escape and the reduction hypotheses are revisited in this new framework. Theoretical considerations suggest that RNA viruses may have originated in the nucleoprotein world by escape or reduction from RNA-cells, whereas DNA viruses (at least some of them) might have evolved directly from RNA viruses. The antiquity of viruses can explain why most viral proteins have no cellular homologues or only distantly related ones. Viral proteins have replaced the ancestral bacterial RNA/DNA polymerases and primase during mitochondrial evolution. It has been suggested that replacement of cellular proteins by viral ones also occurred in early evolution of the DNA replication apparatus and/or that some DNA replication proteins originated directly in the virosphere and were later on transferred to cellular organisms. According to these new hypotheses, viruses played a critical role in major evolutionary transitions, such as the invention of DNA and DNA replication mechanisms, the formation of the three domains of life, or else, the origin of the eukaryotic nucleus.

Amino Acid Sequence↗
PubMed1999

Decline of simian immunodeficiency virus (SIV)-specific cytotoxic T lymphocytes in the peripheral blood of long-term nonprogressing macaques infected with SIVmac32H-J5.

The evolution of simian immunodeficiency virus (SIV)-specific cytotoxic T lymphocyte precursors (CTLps) and their relationship with virus replication were studied in SIV-infected macaques. After primary viremia, 3 of 8 macaques lost culturable virus and polymerase chain reaction-detectable provirus in peripheral blood. Although proviral DNA persisted in the spleen and lymph nodes, virus loads were below or barely above detection levels. Throughout the study, the 3 macaques remained asymptomatic, with stable CD4+ cell counts. These findings were associated with the detection of CTLps directed against both structural and regulatory SIV proteins. The response peaked during the first 7 months of infection but waned subsequently. CTLps increased after rechallenge of 1 macaque, suggesting that limited antigenic stimulation contributed to their disappearance from circulation. Transient viremia with increasing CTLp frequencies and antibody titers also suggested at least partial susceptibility to reinfection. These findings bear implications for vaccination strategies aimed at inducing protective CTLs against lentiviruses.

Animals↗
PubMed1996

Is hepatitis C virus-RNA detection by nested polymerase chain reaction clinically relevant in hemodialysis patients?

We have prospectively studied in hemodialysis (HD) patients the evolution of hepatitis C virus (HCV) viremia and the putative relationships between the viremia and the biological markers of liver disease. For each of 22 HD patients having detectable antibodies to HCV (anti-HCV+), we looked four times for serum HCV-RNA by nested PCR (N-PCR), in April and November 1992, November 1993 and May 1994. We checked the transaminases (Trans) and the gamma glutamyl transpeptidase (gamma(GT)) levels on the same day as blood tests for the N-PCR. Abnormal Trans or gamma(GT)++ values were considered if they exceeded the upper limit of the normal level for our laboratory. Fifteen patients (68%) were intermittently N-PCR positive (N-PCR+): 3 patients were N-PCR+ at three determinations, 7 were N-PCR+ at two determinations and 5 only one time. Two patients (9%) were always N-PCR+ and five (23%) always negative. No correlation between an abnormal value of either Trans or gamma(GT) and viremia was evidenced at successive determinations. In conclusion, the majority (68%) of the anti-HCV+ patients had intermittent HCV N-PCR+. Among the anti-HCV+ patients, 77% were viremic. Since HCV viremia is often transitory and since there is no correlation between N-PCR positivity and the increase in Trans or gamma(GT) activities, HCV-RNA detection by N-PCR is probably not clinically relevant in anti-HCV+ HD patients.

Alanine Transaminase↗
PubMed1977

Evolutionary relationships between gag gene-coded proteins of murine and primate endogenous type C RNA viruses.

Several low molecular weight proteins of endogenous type C viruses of the RD114/baboon group are compared with the gag gene translational products of endogenous type C viruses of murine origin. The p10 proteins of each virus group are shown to be immunologically and biochemically related, while the p12 proteins of RD114/baboon viruses are demonstrated to share antigenic determinants with murine viral p15. Moreover, highly type-specific phosphoproteins, p15 of RD114/baboon viruses and p12 of murine viruses, are shown to possess very similar biochemical properties. These findings, along with previous studies indicating immunologic cross-reactivity between their major internal antigens, p30, demonstrate that each of the gag gene-coded proteins of murine type C viruses has a analogue in viruses of the RD114/baboon group. The immunologic and biochemical relatedness of their gag gene translational products supports the concept of a common progenitor in the evolution of these endogenous viruses.

Animals↗
PubMed1995

Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression.

Phylogenetic analysis was used to study in vivo genetic variation of the V3 region of human immunodeficiency virus type 1 in relation to disease progression in six infants with vertically acquired human immunodeficiency virus type 1 infection. Nucleotide sequences from each infant formed a monophyletic group with similar average branch lengths separating the sets of sequences. In contrast to the star-shaped phylogeny characteristic of interinfant viral evolution, the shape of the phylogeny formed by sequences from the infants who developed AIDS tended to be linear. A computer program, DISTRATE, was written to analyze changes in DNA distance values over time. For the six infants, the rate of divergence from the initial variant was inversely correlated with CD4 cell counts averaged over the first 11 to 15 months of life (r = -0.87, P = 0.024). To uncover evolutionary relationships that might be dictated by protein structure and function, tree-building methods were applied to inferred amino acid sequences. Trees constructed from the full-length protein fragment (92 amino acids) showed that viruses from each infant formed a monophyletic group. Unexpectedly, V3 loop protein sequences (35 amino acids) that were found at later time points from the two infants who developed AIDS clustered together. Furthermore, these sequences uniquely shared amino acids that have been shown to confer a T-cell line tropic phenotype. The evolutionary pattern suggests that viruses from these infants with AIDS acquired similar and possibly more virulent phenotypes.

Acquired Immunodeficiency Syndrome↗
PubMed1992

Evolutionary relationships among the gnat-transmitted orbiviruses that cause African horse sickness, bluetongue, and epizootic hemorrhagic disease as evidenced by their capsid protein sequences.

The amino acid sequences of four major capsid proteins of African horse sickness virus (serotype 4, AHSV-4) have been compared with those of Bluetongue virus of sheep. Epizootic hemorrhagic disease virus of deer, and the phylogenetic relationships established. Complete nucleotide sequence analysis of three RNA segments (L2, L3, and M6) of AHSV-4 and their encoded products, VP2, VP3, and VP5, together with previously published data for VP7 (Roy et al., 1991), have revealed that of the four capsid proteins the innermost protein, VP3, is the most conserved, and the outermost protein, VP2, is the most variable. Some 57-58% of the aligned BTV-10 and EHDV-1 VP3 amino acids are identical with those of AHSV-4. This compares to an identity of 79% between the BTV and EHDV VP3 sequences. For the VP7 proteins 64% of the aligned amino acids are identical between BTV-10 and EHDV-1, while they share 44-46% amino acid residues with the aligned VP7 protein of AHSV-4. By contrast, the VP2 proteins of the three viruses share only 19-24% identical amino acids. Various other comparative analyses of the proteins indicate that the VP2 species of the three orbiviruses are similar. Unlike VP2, the other outer capsid protein, VP5 is more conserved among the three viruses. On alignment, the VP5 of AHSV-4 has some 43-45% identical amino acids with that of BTV-10 and EHDV-1. Between BTV and EHDV, 62% of the aligned sequences are identical.

African Horse Sickness Virus↗
PubMed1982

Evolution of infectious mononucleosis into Epstein-Barr virus carrying monoclonal malignant lymphoma.

A monoclonal malignant lymphoma was diagnosed in a 30-month-old Japanese boy, who, since the age of 12 months, had had chronic, recurrent infectious mononucleosis manifested by repeated episodes of severe cough and high fever accompanied by marked lymphadenopathy and hepatosplenomegaly and high serum Epstein-Barr virus (EBV) antibody titres. The diagnosis of Burkitt's lymphoma was made when a cervical lymph-node biopsy specimen revealed massive proliferation of immature B-cells with starry-sky histiocytes. These lymph-node cells were characterised by a translocation between chromosomes 10 and 17. There were approximately 9 EBV genome-equivalents per cell. Most cells were positive for nuclear antigen (EBNA); early antigen (EA) and viral capsid antigen (VCA) were also detected. The presence of EBV was supported by finding that the cell-free lymph-node extract transformed cord-blood lymphocytes into EBNA-positive blast cells. The proportion of EA-positive and VCA-positive cells increased rapidly in culture for 24 h, then the positive cells degenerated rapidly and completely. The cells also contained numerous herpes-type virus particles. The child improved considerably with cytostatic treatment and has been in remission for 2 years.

Antibodies, Viral↗
PubMed1999

Evolution of the hypervariable region of hepatitis C virus.

Despite being the most intensively studied part of the hepatitis C virus genome, our understanding of the function of the hypervariable region (HVR) at the NH2-terminus of the E2 protein remains very limited. During chronic infection the HVR usually changes over time, with changes usually mirrored by those of HVR-specific antibodies. Evidence is presented suggesting that the HVR is subject to constraint in its length, amino acid composition, and in the amino acid replacements that are tolerated at different positions. These constraints, and the pattern of HVR variation during chronic infection, suggest that it has an important role in virus infection. A causal relationship between HVR variation and persistence of HCV remains to be demonstrated.

Amino Acid Sequence↗
PubMed1994

Herpes simplex virus infections of women and their offspring: implications for a developed society.

Herpes simplex virus infections of humans have been known since ancient times. Contemporary society has witnessed a series of devastating manifestations of herpes simplex virus infections--namely, genital herpes simplex virus infection and neonatal herpes simplex virus infection. With the evolution of society, particularly advances in birth control and increasing promiscuity, the seroprevalence of herpes simplex virus type 2 infections has increased worldwide, however, more so in developed societies. As a consequence, individuals of child-bearing age are at risk for either reactivation of herpes simplex virus at termination of gestation or acquisition of a new primary infection at that time. The consequences of vertical transmission of herpes simplex virus from mother to child, resulting in neonatal herpes simplex virus infection, can be devastating. Current efforts, which are directed toward the treatment of neonatal herpes, have established the value of drugs such as vidarabine and acyclovir. However, the real emphasis for future programs is the prevention of herpes simplex virus infections to avoid person-to-person transmission either horizontally or vertically. The development of vaccines directed against herpes simplex virus may be of value toward this end.

Antiviral Agents↗
PubMed2001

Evolution of depressive symptoms in human immunodeficiency virus-infected patients entering primary care.

Our purpose was to examine among HIV-infected patients a) characteristics associated with depressive symptoms at initial primary care presentation and b) factors associated with improvement in depressive symptoms. We interviewed HIV-infected patients at initial presentation and reassessed them 6 months later. At baseline and follow-up, we collected data on depressive symptoms (CES-D) and other characteristics. Using multiple linear regression, we examined associations between CES-D score and baseline variables. We used multiple logistic regression to examine factors associated with improvement in depressive symptoms. Seventy-one percent of the baseline sample (N = 203) scored above the threshold considered indicative of depression. At 6 months, 36% of the subjects who were followed improved in depressive symptoms. Higher baseline CES-D scores, improvements in HIV-related symptoms, and joining a support group were associated with improvement. Depressive symptoms in this urban HIV-infected population were highly prevalent. It is essential to screen, identify, and treat depression among patients entering care for HIV disease. Encouragement in joining support groups is a reasonable component of a strategy for addressing this common condition.

Adult↗
PubMed1989

Biological and genetic evolution of the nucleoprotein gene of human influenza A viruses.

There is a significant difference in the ability of human influenza A virus H1N1 strains isolated up to 1977 and those isolated later to rescue temperature-sensitive mutants of fowl plague virus with a defect in the nucleoprotein (NP) gene. Therefore the NP genes of five human H1N1 and H3N2 influenza A virus strains, isolated between 1950 and 1978, have been sequenced. By comparison with previous and more recent isolates, an evolutionary pathway has been established. Three amino acid replacements were found which might be responsible for the functional difference between the USSR (1977) and the Brazil (1978) strains. The California (H1N1) strain isolated in 1978 had acquired by reassortment the NP gene of a human H3N2 virus circulating at about 1977 as had been previously suggested by investigations involving RNase fingerprint or hybridization techniques.

Amino Acid Sequence↗
PubMed2006

Increasing appearance of reassortant influenza B virus in Taiwan from 2002 to 2005.

Genetic and antigenic analyses of influenza B virus field strains isolated in Taiwan from 1998 to 2005 were performed. To investigate the molecular evolution of influenza B viruses, sequence analysis of the hemagglutinin (HA1 subunit) and neuraminidase genes was performed. All influenza B viruses isolated between 1998 and 2000 belonged to the B/Yamagata/16/88 lineage. The B/Victoria/2/87 lineage, which was cocirculating with the Yamagata lineage, was identified in Taiwan in March 2001. Concurrently, there was an increasing prevalence of this lineage in many parts of the world, including North America and Europe, during the 2001-2002 season. Since 2002, genetic reassortants of influenza B virus with the Victoria lineage of hemagglutinin and the Yamagata lineage of neuraminidase have been found at a rate of 46%. Therefore, in 2002, at least three sublineages of influenza B virus strains, the B/Shanghai/361/2002-like strain (Yamagata lineage), the B/Hong Kong/330/01-like strain (Victoria lineage), and the B/Hong Kong/1351/02-like strain (B reassortant lineage), were identified in Taiwan. The results showed that genetically distinct lineages can cocirculate in the population and that the reassortment among these strains plays a role in generating the genetic diversity of influenza B viruses. Interestingly, from January to April 2005, B reassortant viruses became dominant (73%) in Taiwan, which indicated that a mismatch had occurred between the influenza B vaccine strain recommended for the 2004-2005 season in the Northern hemisphere by the World Health Organization and the epidemic strain.

Antigens, Viral↗
PubMed1995

Evolution of rifampin resistance in human immunodeficiency virus-associated tuberculosis.

Acquired rifampin resistance without preexisting isoniazid resistance is highly unusual in patients with tuberculosis. The purpose of this report is to describe and characterize that unusual pattern of acquired drug resistance in three patients with human immunodeficiency virus (HIV) infection. The patients originally had Mycobacterium tuberculosis strains that were susceptible to isoniazid and rifampin. During treatment in two patients and after completion of therapy in the remaining one, each patient developed active, rifampin-resistant, isoniazid-susceptible tuberculosis. One patient subsequently developed isoniazid resistance also. Studies on patients' M. tuberculosis isolates using IS6110 restriction fragment length polymorphism typing and rpoB gene sequencing indicated that rifampin resistance in each patient arose during therapy by an rpoB gene mutation in the original M. tuberculosis isolate. Detection of this unusual drug-resistance phenotype in three patients with HIV infection suggests that acquired rifampin resistance is somehow associated with co-infection due to HIV and tuberculosis.

AIDS-Related Opportunistic Infections↗