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PubMed2005

Newer respiratory virus infections: human metapneumovirus, avian influenza virus, and human coronaviruses.

PURPOSE OF REVIEW: Recently, several previously unrecognized respiratory viral pathogens have been identified and several influenza A virus subtypes, previously known to infect poultry and wild birds, were transmitted to humans. Here we review the recent literature on these respiratory viruses. RECENT FINDINGS: Human metapneumovirus has now been detected worldwide, causing severe respiratory tract illnesses primarily in very young, elderly and immunocompromised individuals. Animal models and reverse genetic techniques were designed for human metapneumovirus, and the first vaccine candidates have been developed. Considerable genetic and antigenic diversity was observed for human metapneumovirus, but the implication of this diversity for vaccine development and virus epidemiology requires further study. Two previously unrecognized human coronaviruses were discovered in 2004 in The Netherlands and Hong Kong. Their clinical impact and epidemiology are largely unknown and warrant further investigation. Several influenza A virus subtypes were transmitted from birds to humans, and these viruses continue to constitute a pandemic threat. The clinical symptoms associated with these zoonotic transmissions range from mild respiratory illnesses and conjunctivitis to pneumonia and acute respiratory distress syndrome, sometimes resulting in death. More basic research into virus ecology and evolution and development of effective vaccines and antiviral strategies are required to limit the impact of influenza A virus zoonoses and the threat of an influenza pandemic. SUMMARY: Previously unknown and emerging respiratory viruses are an important threat to human health. Development of virus diagnostic tests, antiviral strategies, and vaccines for each of these pathogens is crucial to limit their impact.

Communicable Diseases, Emerging↗
PubMed2006

Comparison of in vitro replication features of H7N3 influenza viruses from wild ducks and turkeys: potential implications for interspecies transmission.

In previous work, it was shown that turkey H7N3 influenza viruses, presumably derived 'in toto' from interspecies transmission of duck viruses in Northern Italy, had only 2 aa differences in haemagglutinin and a few amino acid differences as well as a 23 aa deletion in neuraminidase compared with duck viruses. Here, the replication of these duck and turkey viruses in Madin-Darby canine kidney cells was investigated with respect to virus-cell fusion and viral elution from red blood cells. Duck viruses showed similar receptor-binding properties to turkey viruses but possessed a higher pH of fusion activation than the turkey viruses. Conversely, turkey viruses were not able to elute from red blood cells. These data confirm that neuraminidase-stalk deletion impairs the release of virions from cells and also confirm existence of naturally occurring viruses with different pH fusion activities, raising the possibility that these features may play a role in the evolution of influenza viruses in different hosts.

Animals↗
PubMed2005

Limited sequence evolution within persistently targeted CD8 epitopes in chronic human immunodeficiency virus type 1 infection.

Studies in acute human immunodeficiency virus type 1 (HIV-1) infection indicate viral evolution under CD8 T-cell immune selection pressure, but the effects of ongoing immune pressure on epitope evolution during chronic infection are not well described. In this study, we performed a detailed longitudinal analysis of viral sequence variation within persistently targeted cytotoxic T-lymphocyte (CTL) epitopes in two HIV-1-infected persons during 6 years of persistent viremia. Responses were quantitated using freshly isolated peripheral blood lymphocytes in direct lytic assays as well as by gamma interferon (IFN-gamma) Elispot assays on cryopreserved cells. Seven targeted epitopes were identified in each person. In the majority of cases, the dominant epitope sequence did not change over time, even in the presence of responses of sufficient magnitude that they were detectable using fresh peripheral blood mononuclear cells in direct lytic assays. Only 4 of the 14 autologous epitopes tested represented potential CTL escape variants; however, in most cases strong responses to these epitopes persisted for the 6 years of study. Although persistent IFN-gamma responses were detected to all epitopes, direct lytic assays demonstrated declining responses to some epitopes despite the persistence of the targeted sequence in vivo. These data indicate limited viral evolution within persistently targeted CD8 T-cell epitopes during the chronic phase of infection and suggest that these regions of the virus are either refractory to sequence change or that persistently activated CD8 T-cell responses in chronic infection exert little functional selection pressure.

Acquired Immunodeficiency Syndrome↗
PubMed1983

Evolution of the nucleotide sequence of influenza virus RNA segment 7 during drift of the H3N2 subtype.

The complete genetic information contained in the influenza virus RNA segment 7 of the A/Bangkok/1/79 (H3N2) strain has been cloned by in vitro synthesis of the complementary dsDNA and its insertion into plasmid pBR322. The nucleotide sequence of the viral RNA segment has been determined from the cDNA insert. It is 1027 nucleotides long, and contains two open reading frames, as shown for other influenza virus strains. When compared with the previously published sequence for the A/Udorn/72 (H3N2) strain, 15 nucleotide exchanges are observed, most of them silent mutations, and only two causing amino acid changes in each of the M1 and M2 protein sequences.

Amino Acid Sequence↗
PubMed2003

Evidence for recombination in the envelope gene of maedi-visna virus.

Frequent recombination occurs during replication in all retroviruses examined. This increases the genetic variation in the retroviral population and may be of importance in the evolution of the virus. Maedi-visna virus (MVV), a retrovirus of sheep, has a highly variable envelope gene. In a previous experiment, 20 sheep were infected with an uncloned strain of MVV and virus was isolated at regular intervals for 7 years. We sequenced the envelope genes of a number of these strains and found evidence for recombination that may have contributed to the observed high frequency of antigenic variants.

Animals↗
PubMed1999

[Progressive multifocal leukoencephalopathy associated with human immunodeficiency virus infection: the clinical, neuroimaging, virological and evolutive characteristics in 35 patients].

BACKGROUND: The clinical, neuroimaging, virologic and evolutive characteristics of progressive multifocal leukoencephalopathy (PML) in 35 AIDS patients are studied. PATIENTS AND METHODS: PML was diagnosed by clinical and neuroimaging criteria in 32 patients and by autopsy in other three. The detection of JC virus (JCV) was done by PCR and further hybridization of the amplified DNA in peripheral blood lymphocytes, urine and CSF. RESULTS: 127 of 930 HIV positive patients were admitted by neuropsychiatric symptoms and of them 35 (SD 27.6%) by PML. The PML patients had a mean CD4 lymphocytes count of 75.3 (82.0)/x 10(6)/l and a HIV viral load of 330,698 (538,971) copies of RNA/ml. Thirty patients did not receive any anti-retroviral therapy or only transcriptase inhibitors monotherapy and five triple anti-retroviral therapy, including a proteases inhibitor. Multiple hypodense lesions on CT (53.1%) and T2 hyperintense lesions on MRI (58.3%) were the most frequent neuroimaging findings. JCV was detected in 20/21 (95.2%) LMP patients: 18/19 detections in lymphocytes, 6/8 in CSF and 4/6 in urine. The mean survival without and with antiretroviral therapy were 3.0 (0.47) and 21.4 (4.4) months (p < 0.001) in 34 patients followed. PML progressed to death in 31/34 patients (91.2%), and remained stable in 3/34 (8.8%). A patient was lost for follow-up. CONCLUSIONS: The application of clinical and neuroimaging criteria and the detection of JCV in CSF are useful for high presumption diagnosis of PML without brain biopsies. JCV detection in lymphocytes and in urine have a much lower predictive value. The evolution and survival of this disease can improve with triple anti-retroviral therapy including a protease inhibitor.

AIDS-Related Opportunistic Infections↗
PubMed2000

Evolutionary dynamics of HTLV-I.

Using mathematical models to describe the in vivo dynamics of HTLV-I infection, an explanation is offered for the slow rate of evolution of HTLV-I relative to HIV-1. In agreement with experimental findings, it is assumed that cell activation is required for successful replication in T helper cells and that HTLV-I induces a significant degree of bystander activation. It is found that the rate of evolution of HTLV-I is limited by the restricted availability of activated uninfected T cells, both at high and low proviral loads. This limits the within-host sequence diversity of HTLV-I and may therefore account for the slow rate of evolution of the virus in the population. Specific differences in the in vivo dynamics of HTLV-I and HIV-1 are identified which may account for the discrepancy in the rate of evolution of these two retroviruses.

Evolution, Molecular↗
PubMed2006

Reassortment between human A(H3N2) viruses is an important evolutionary mechanism.

Phylogenetic relationships of whole genomes of H3N2 viruses circulating in Germany during a 6-year period from 1998 to 2005 revealed the co-circulation of different lineages of viruses. Multiple reassortment events occurred during this time between viruses belonging to different lineages or different subgroups. Strains isolated during 1998-1999 were characterised by a surprisingly high heterogeneity and multiple reassortment events. Seventy percent of the examined 1998-1999 viruses had completely different genome compositions. To our knowledge, such an exceptional high proportion of different reassortant strains, encompassing all eight genome segments, have not been described before. In contrast, only one reassortant virus was prevalent during 1999-2000 even though two of the three 1998-1999 lineages were co-circulating. Reassortant viruses were isolated also in each of the other seasons. However, the proportion of H3N2 viruses with different genome compositions varied from season to season. Strains with a reassortant NA played an important role and were also detected during 2003-2004 and 2004-2005 accounting for 45% and 70% of the circulating H3N2 viruses, respectively. Moreover, different reassortment events occurring during these seasons included also the PB1, PB2 and NP genes. The results presented here emphasize that genetic reassortment is an important factor in the evolution of H3N2 viruses and highlight the need for a comprehensive analysis of influenza viruses, especially with regard to the annual vaccine composition.

Biological Evolution↗
PubMed2003

The extent of homologous recombination in members of the genus Flavivirus.

The family Flaviviridae includes important human pathogens, such as dengue (DEN) virus, yellow fever (YF) virus and hepatitis C virus, many of which have emerged or re-emerged in recent years. Until recently, flavivirus evolution was thought to proceed in a clonal manner, with diversity generated mainly through the accumulation of mutational changes. However, this assumption has now been shown to be invalid, with homologous recombination demonstrated in all three genera of the FLAVIVIRIDAE: Since recombination has important implications for the study of virus evolution, a survey of recombination in the viruses of the genus Flavivirus was carried out. Using envelope gene sequence data and a combination of graphical and phylogenetic analyses, hitherto unreported recombination in Japanese encephalitis virus and St Louis encephalitis virus was detected, as well as further recombinants in DEN virus. However, no evidence for recombination was found in West Nile or YF viruses, or in the tick-borne flavivirus group. It is proposed that the difference between the mosquito- and tick-borne viruses can be accounted for by their differing modes of transmission, whilst the variation among the mosquito-borne flaviviruses reflects both the ecology of the particular host and vector species and also bias in the sampling process.

Dengue Virus↗
PubMed2006

Distinct viral populations differentiate and evolve independently in a single perennial host plant.

The complex structure of virus populations has been the object of intensive study in bacteria, animals, and plants for over a decade. While it is clear that tremendous genetic diversity is rapidly generated during viral replication, the distribution of this diversity within a single host remains an obscure area in this field of science. Among animal viruses, only Human immunodeficiency virus and Hepatitis C virus populations have recently been thoroughly investigated at an intrahost level, where they are structured as metapopulations, demonstrating that the host cannot be considered simply as a "bag" containing a homogeneous or unstructured swarm of mutant viral genomes. In plants, a few reports suggested a possible heterogeneous distribution of virus variants at different locations within the host but provided no clues as to how this heterogeneity is structured. Here, we report the most exhaustive study of the structure and evolution of a virus population ever reported at the intrahost level through the analysis of a Prunus tree infected by Plum pox virus for over 13 years following a single inoculation event and by using analysis of molecular variance at different hierarchical levels combined with nested clade analysis. We demonstrate that, following systemic invasion of the host, the virus population differentiates into several distinct populations that are isolated in different branches, where they evolve independently through contiguous range expansion while colonizing newly formed organs. Moreover, we present and discuss evidence that the tree harbors a huge "bank" of viral clones, each isolated in one of the myriad leaves.

Evolution, Molecular↗
PubMedDate not supplied

[Evolution of hematological parameters in a group of children with human immunodeficiency virus infection - HIV 1]

OBJECTIVE: To analyze the evolution of clinical and hematological aspects of the children infected with HIV 1. METHODS: Using the CDC criteria, 1994, 37 children with HIV infection were selected, followed up at the Immunodeficiency Clinic at UNICAMP. The study is longitudinal descriptive. Complete blood count, ferritin, serum iron, TIBC and direct Coombs were carried out. RESULTS: The clinical category that predominated wasB(45.94%) and categories A and C were equal (27.03%). All of them were having antiretroviral therapy. Hypochromic and microcytic anemia were seen in 100% of patients up to 12 months of age. There was association between anemia and the progression of the disease, both clinical (p=0.031) and immunological (p=0.0027) and with lymphopenia too (p=0.033). Thrombocytopenia occurred in 10 to 25% of the patients. Low serical ferritin was seen in 2.7% of the cases and low serum iron in 11.1%. All the 15 patients analyzed had negative Coombs test. There was weight and height reduction in 23.5 to 45% of the children and 70.3% had clinical manifestations up to 9 months of age. During the follow up 13.2% of the patients died. CONCLUSIONS: There was association between anemia and lymphopenia with the progression of the disease. In relation to the aetiology of the anemia, about 10% can be considered anemia of chronic disease. Probably the hematological abnormalities seen in peripheral blood are the consequences of loss of control of cellular death mechanism and hematopoiesis in individuals infected by HIV 1.

Journal Article↗
PubMed2004

Modelling HIV-RNA viral load in vertically infected children.

Human immunodeficiency virus (HIV) ribo-nucleic acid (RNA) viral load is a measure of actively replicating virus and is used as a marker of disease progression. For a thorough understanding of the dynamics of the evolution of the virus in the early life of HIV-1 vertically infected children, it is important to elucidate the pattern of HIV-RNA viral load over age. An aspect of assay systems used in the quantification of RNA viral load is that they measure values above particular cut-off values for detection, below which the assays used are not sufficiently sensitive. In this way, measurements are potentially left-censored. Recent adult studies suggest that to adequately model RNA pattern over age, it is necessary to account for within-subject correlation, due to repeated measures, and censoring. The aim of this study, therefore, was to establish whether it is necessary to use complex methods to allow for repeated measures within individuals and censoring of the HIV-RNA viral load in children enrolled in a cohort study. The approach involved the identification of an appropriate model for the basic pattern of RNA viral load by age and subsequent assessment of various estimation procedures accounting for repeated measures and censoring in different ways. Methods developed by Hughes involving the expectation-maximization (EM) algorithm and the Gibbs sampler were taken as the benchmark for comparison of simpler alternatives. Other approaches considered involve linear mixed-effects and ordinary least squares in which censoring is dealt with informally by taking the cut-off value as absolute or taking the mid-point between cut-off and zero. Fractional polynomials provided a substantially superior approach for modelling the dynamics of viral load over age compared to conventional polynomials or change-point models. Allowing for repeated measures was necessary to improve the power of the likelihood ratio tests required to establish the final model, but methods beyond taking the mid-point for censored values did not further improve the fit. Although Hughes' methodology is the best approach, its implementation is not necessary for the identification of the optimal model.

Algorithms↗
PubMed1997

[Antigenic drift of type A and B influenza viruses].

Epidemics of influenza of the past 10 years were reviewed by integrating records from Morbidity and Mortality Weekly Reports of the United States and Infectious Agents Surveillance Reports in Japan, as well as data of antigenic drift of epidemic strains. Nucleotide-sequencing analyses of field isolates have shown characteristic amino acid substitutions in their hemagglutinin molecules, and phylogenetic analyses have indicated evolutionary relationships among the viruses. Integration of information obtained from both epidemics and molecular analyses would help our understanding of antigenic drift and evolution of influenza viruses.

Antigenic Variation↗
PubMedDate not supplied

Association of avian reovirus M and S genes with viral behavior in vivo. II. Viral pathogenicity.

A group of avian reoviruses comprising serially passaged S1133 strains and their vaccine derivatives was examined biochemically to study the temporal evolution of the viruses and biologically to assess their relative pathogenicities. The strains fell into three groups of differing virulence, the viruses becoming less pathogenic the longer they were passaged. Protein and RNA profiles of the strains showed no distinct patterns of evolution nor any trend that could be correlated with pathogenicity. Nucleic acid hybridization studies of the strains indicated that all the genes were altered to some extent during passage. The S1 and M3 genes appeared to change the most during the first half of passage history, but later, as the virus was cold-adapted or passaged extensively, the M2, S2, and S3 genes also appeared to vary. When viruses were grouped according to virulence, the greatest changes were seen in the S1, M2, and M3 genes, suggesting that these may be associated with the virulence of a given avian reovirus strain.

Animals↗
PubMed2005

Evidence of genetic variability of human immunodeficiency virus type 1 in plasma and cervicovaginal lavage in ethiopian women seeking care for sexually transmitted infections.

Most human immunodeficiency virus type 1 (HIV-1) transmission in developing countries occurs through heterosexual intercourse or during birth from mother to child. It is critical to characterize the virus of the genital tract variants as a target for the development of an HIV-1 vaccine and microbicidal therapies. We compared the C2V3 env domain genetic diversity of HIV-1 in female genital secretions and in plasma from Ethiopian women seeking care for sexually transmitted infections (STIs). Sequences within an individual differed between the plasma and cervicovaginal lavage (CLV) compartments with nucleotide and amino acid median difference values of 8.3 and 4.8%, respectively. Sequence diversity in CVL was greater than in plasma. And the V3 loop positive charge was often more elevated in CVL. These are markers of the differential evolution of the viruses in CVL and peripheral blood indicating that limited evolution at the site of contact is not the limiting factor determining the preferential transmission of macrophage tropic viruses.

Amino Acid Sequence↗
PubMed2006

Molecular diversity of rabies viruses associated with bats in Mexico and other countries of the Americas.

Bat rabies and its transmission to humans and other species in Mexico were investigated. Eighty-nine samples obtained from rabid livestock, cats, dogs, and humans in Mexico were studied by antigenic typing and partial sequence analysis. Samples were further compared with enzootic rabies associated with different species of bats in the Americas. Patterns of nucleotide variation allowed the definition of at least 20 monophyletic clusters associated with 9 or more different bat species. Several lineages associated with distinctive antigenic patterns were found in rabies viruses related to rabies in vampire bats in Mexico. Vampire bat rabies virus lineages associated with antigenic variant 3 are widely spread from Mexico to South America, suggesting these lineages as the most likely ancestors of vampire bat rabies and the ones that have been moved by vampire bat populations throughout the Americas. Rabies viruses related to Lasiurus cinereus, Histiotus montanus, and some other not yet identified species of the genus Lasiurus were found circulating in Mexico. Long-range dissemination patterns of rabies are not necessarily associated with migratory bat species, as in the case of rabies in Desmodus rotundus and Histiotus montanus. Human rabies was associated with vampire bat transmission in most cases, and in one case, rabies transmission from free-tailed bats was inferred. The occurrence of rabies spillover from bats to domestic animals was also demonstrated. Genetic typing of rabies viruses allowed us to distinguish trends of disease dissemination and to address, in a preliminary fashion, aspects of the complex evolution of rabies viruses in different host-reservoir species.

Amino Acid Sequence↗
PubMed1992

Heterogeneity of the mutation rates of influenza A viruses: isolation of mutator mutants.

The rates of mutation to the mar (monoclonal antibody-resistant) genotype of individual influenza virus plaque isolates, obtained from a stock generated after two successive cloning steps, have been determined by the fluctuation test. When a random sample of 60 clones was analyzed, 7 contained a proportion of mar mutants significantly higher than the average, and among them, 2 showed a mutation rate two to three times higher than the average value obtained for the virus population when the hemagglutinin-specific monoclonal antibody 2G10 was used. In order to look for mutants with higher mutation rates, a systematic search was carried out with a nonmutagenized virus stock, and several clones with increased mutation rates were isolated. One of them (mut43) was characterized further and was shown to have a mutation rate three to four times higher than that of the virus population at the sites defined by two nonoverlapping, hemagglutinin-specific monoclonal antibodies as well as at the site defined by a neuraminidase-specific monoclonal antibody. These results indicate that the mutation rate of an influenza virus is a weighted average of the contributions of a heterogeneous population. The consequences of this fact for the adaptive evolution of influenza viruses are discussed.

Antibodies, Monoclonal↗