Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B

Infectious bursal disease virus (IBDV) is a birnavirus causing immunosuppressive disease in chickens. Emergence of the very virulent form of IBDV (vvIBDV) in the late 1980s dramatically changed the epidemiology of the disease. In this study, we investigated the phylogenetic origins of its genome segments and estimated the time of emergence of their most recent common ancestors. Moreover, with recently developed coalescence techniques, we reconstructed the past population dynamics of vvIBDV and timed the onset of its expansion to the late 1980s. Our analysis suggests that genome segment A of vvIBDV emerged at least 20 years before its expansion, which argues against the hypothesis that mutation of genome segment A is the major contributing factor in the emergence and expansion of vvIBDV. Alternatively, the phylogeny of genome segment B suggests a possible reassortment event estimated to have taken place around the mid-1980s, which seems to coincide with its expansion within approximately 5 years. We therefore hypothesize that the reassortment of genome segment B initiated vvIBDV expansion in the late 1980s, possibly by enhancing the virulence of the virus synergistically with its existing genome segment A. This report reveals the possible mechanisms leading to the emergence and expansion of vvIBDV, which would certainly provide insights into the scope of surveillance and prevention efforts regarding the disease.

[Christopher Columbus flu. A hypothesis for an ecological catastrophe]

When Christopher Columbus and his men embarked on the second Colombian expedition to the New World (1493), the crew suffered from fever, respiratory symptoms and malaise. It is generally accepted that the disease was influenza. Pigs, horses and hens acquired in Gomera (Canary Islands) traveled in the same ship. The pigs may well have been the origin of the flu and the intermediary hosts for genetic recombination of other viral subtypes. The Caribbean archipelago had a large population of birds, the natural reservoir of the avian influenza virus. In this ecological scenario there was a concurrence of several biological elements that had never before coexisted in the New World: pigs, horses, the influenza virus and humans. We propose that birds are likely to have played an important role in the epidemiology of the flu occurring on the second Colombian trip, which caused a fatal demographic catastrophe, with an estimated mortality of 90% among the natives.

Rapid dissemination of a pathogenic simian/human immunodeficiency virus to systemic organs and active replication in lymphoid tissues following intrarectal infection

A better understanding of virological events during the early phase of human immunodeficiency virus 1 (HIV-1) infection is important for development of effective antiviral vaccines. In this study, by using quantitative PCR and an infectious plaque assay, virus distribution and replication were examined in various internal organs of rhesus macaques for almost 1 month after intrarectal inoculation of a pathogenic simian immunodeficiency virus/HIV chimeric virus (SHIV-C2/1-KS661c). At 3 days post-inoculation (p.i.), proviral DNA was detected in the rectum, thymus and axillary lymph node. In lymphoid tissues, infectious virus was first detected at 6 days p.i. and a high level of proviral DNA and infectious virus were both detected at 13 days p.i. By 27 days p.i., levels of infectious virus decreased dramatically, although proviral DNA load remained unaltered. In the intestinal tract, levels of infectious virus detected were much lower than in lymphoid tissues, whereas proviral DNA was detected at the same level as in lymphoid tissues throughout the infection. In the thymus and jejunum, CD4CD8 double-positive T cells were depleted earlier than CD4 single-positive cells. These results show that the virus spread quickly to systemic tissues after mucosal transmission. Thereafter, infectious virus was actively produced in the lymphoid tissues, but levels decreased significantly after the peak of viraemia. In contrast, in the intestinal tract, infectious virus was produced at low levels from the beginning of infection. Moreover, virus pathogenesis differed in CD4 single-positive and CD4CD8 double-positive T cells.

Very virulent infectious bursal disease virus: reduced pathogenicity in a rare natural segment-B-reassorted isolate

The purpose of this study was to compare the molecular epidemiology of infectious bursal disease virus (IBDV) segments A and B of 50 natural or vaccine IBDV strains that were isolated or produced between 1972 and 2002 in 17 countries from four continents, with phenotypes ranging from attenuated to very virulent (vv). These strains were subjected to sequence and phylogenetic analysis based on partial sequences of genome segments A and B. Although there is co-evolution of the two genome segments (70 % of strains kept the same genetic relatives in the segment A- and B-defined consensus trees), several strains (26 %) were identified with the incongruence length difference test as exhibiting a significantly different phylogenetic relationship depending on which segment was analysed. This suggested that natural reassortment could have occurred. One of the possible naturally occurring reassortant strains, which exhibited a segment A related to the vvIBDV cluster whereas its segment B was not, was thoroughly sequenced (coding sequence of both segments) and submitted to a standardized experimental characterization of its acute pathogenicity. This strain induced significantly less mortality than typical vvIBDVs; however, the mechanisms for this reduced pathogenicity remain unknown, as no significant difference in the bursal lesions, post-infectious antibody response or virus production in the bursa was observed in challenged chickens.

[Molecular characterization of human influenza viruses--a look back on the last 10 years]

Influenza A (H3N2) viruses and influenza B viruses have caused more than 90% of influenza infections in Germany during the last then years. Continuous and extensive antigenic variation was evident for both the hemagglutinin (HA) and neuraminidase (NA) surface proteins of H3N2 and influenza B viruses. Molecular characterisation revealed an ongoing genetic drift even in years when the antigenic profiles of circulating strains were indistinguishable from those of the previous season. Retrospective phylogenetic studies showed that viruses similar to vaccine strains circulated one or two years before a given strain was recommended as vaccine strain. New drift variants of H3N2 viruses with significantly changed antigenic features appeared during the seasons 1997/1998 and 2002/2003. Most influenza seasons were characterised by a co-circulation of at least two different lineages of H3N2 viruses. Genetic reassortment between H3N2 viruses belonging to separate lineages caused the different evolutionary pathways of the HA and viruses was responsible for the occurrence of H1N2 viruses during the season 2001/02. This new subtype has been detected only sporadically in Germany. The evolution of influenza B viruses was characterised by the re-emergence of B/Victoria/2/87-lineage viruses and their co-circulation with viruses of the B/Yamagata/16/88-lineage. Reassortant B viruses possessing a Victoria/87-lineage HA and a Yamagata/88-like NA were predominant in Germany during 2002/03 and 2004/05.

Roles of neuraminidase in the initial stage of influenza virus infection

We propose a concept that neuraminidase (NA) promotes virus entry into target cells during the initial stage of viral infection, in addition to the generally accepted concept that influenza virus NA promotes the release of progeny virus from a host cell at the final stage of viral replication. When NA activity was inhibited with specific inhibitors such as zanamivir and oseltamivir carboxylate, infection efficiency of the virus to MDCK and A549 cells was reduced to approximately 1/4 and 1/8, respectively. NA inhibitors did not significantly affect virus binding and envelope fusion activities, when assessed using an erythrocyte and virus system. Since the initial stage of viral infection involves binding of the virus to the target cell, virus entry into an endosome and envelope fusion with the endosomal membrane, our results indicated that NA inhibitors interfered with the virus entry step. Thus, NA is thought to promote virus entry, and thereby enhances infection efficiency.

Citrate-mediated disaggregation of rotavirus particles in RotaTeq® vaccine

For the routine manufacture of live virus vaccines, virus is diluted into a formulation buffer to stabilize it for long-term storage, and to facilitate vaccine administration. The characteristics of this buffer are dependent on the storage temperature of the vaccine, as well as the desired characteristics of the product. The formulation buffer for RotaTeq, Merck's live, pentavalent, oral rotavirus vaccine to prevent rotavirus gastroenteritis was developed as a fully liquid solution that requires no pre-feeding prior to administration, and is stable for 24 months at refrigerated temperatures. In studying the effects of the formulation buffer on the live virus contained within RotaTeq, we observed that the formulation buffer also directly impacts the state of rotavirus aggregation. This observation, termed "the matrix effect," was first noted as an approximately 50% increase in measured in vitro infectivity, following dilution of the virus into the buffer. Subsequent experiments confirmed that citrate in the formulation buffer facilitates the disaggregation of viral particles, likely through a carboxylic-acid mediated interaction. For vaccine manufacture, bulk virus is titered and subsequently diluted to a target concentration for dosing. Aggregation of the virus and subsequent inaccurate measurement of the amount of virus contained in either the bulk sample or in the final dosing container could lead to an inability to accurately predict final vaccine concentrations. Thus, discerning the nature and extent of the matrix effect was key principally for providing an accurate prediction of final virus concentration upon dilution, to ensure a robust manufacturing process. In addition, understanding potential contributions of the formulation buffer to clinical efficacy of the vaccine was critical. Clinical data have confirmed that the citrate-mediated disaggregation had no measurable impact on vaccine safety, immunogenicity, or efficacy.

Reassortment and modification of hemagglutinin cleavage motif of avian/WSN influenza viruses generated by reverse genetics that correlate with attenuation

Avian influenza associated with H9N2 and H5N1 subtypes of avian influenza viruses (AIVs) has raised great concerns in China. To study this problem, reverse genetics has been employed. Three reassortants, rgH9N2, rgH5N1 and rgH5N2, were prepared and compared. Their hemagglutinin (HA) and neuraminidase (NA) genes originated from Chinese AIV isolates of H9N2 or H5N1 subtype, while the rest of their genes were derived from A/WSN/33(H1N1) virus (WSN). In the H5 HA reassortants, the multibasic cleavage site was converted to a monobasic one. The results demonstrated that the reassortants did not produce CPE on MDCK cells in the absence of trypsin, showed egg-adaptation phenotype and stability of HA and NA during consecutive egg passages, and were not lethal to chickens and mice. However, the rgH5N1 reassortant exhibited a residual virulence in terms of lethality to chick embryos and pathogenesis in chickens. It can be concluded that (i) the genetic modification of H5 HA attenuated the H5 reassortants, (ii) the presence of internal WSN proteins contributed to the attenuated properties of the reassortants independently on H5 HA, and (iii) also the overall genome composition contributed to virulence differences. This report provides further contribution of reverse genetics to the knowledge of virulence of influenza viruses.

The genesis of a pandemic influenza virus

Pandemic influenza viruses pose a significant threat to public health worldwide. In a recent Nature paper, Taubenberger et al. (2005) now report remarkable similarities between the polymerase genes of the influenza virus that caused the 1918 Spanish influenza pandemic and those of avian influenza viruses. Meanwhile, Tumpey et al. (2005) reporting in Science show that the reconstructed 1918 Spanish influenza virus kills mice faster than any other influenza virus so far tested.

Application of GFP-tagged Plum pox virus to study Prunus-PPV interactions at the whole plant and cellular levels

The Sharka disease caused by the potyvirus Plum pox virus (PPV) is one of the most serious viral diseases affecting stone fruit trees. The study of PPV/Prunus interaction under greenhouse controlled conditions is space, time, labor consuming. While the PPV/Prunus interactions are now quite well known at the whole plant level, few data however are available on the interactions between the virus and the Prunus host plants at the cellular level. Using a green fluorescent protein (GFP)-tagged M type PPV strain, combined to an in vitro inoculation procedure, we developed a novel tool to track PPV invasion in Prunus persica (peach) cv. GF305 and Prunus armeniaca (apricot) cv. Screara susceptible hosts. Different graft combinations were performed using in vitro-maintained healthy or GFP-tagged PPV infected 'GF305' and 'Screara'. Contact for 30 days in grafts between the inoculum and the genotype to be tested were found sufficient to allow the systemic spread of the recombinant virus: fluorescence from GFP-tagged PPV could easily be detected in the entire plant under a binocular microscope allowing quick and reliable sorting of infected plants. Using a fluorescence stereomicroscopy or confocal microscopy, GFP could also be observed in stem cross-sections especially in epidermis and pith cells. In vitro grafting inoculation with GFP-tagged PPV provides a new and powerful tool to facilitate mid-term virus maintenance. Moreover, this tool will be of special importance in the study of PPV infection dynamics in Prunus, allowing as well precise observations of cellular events related to PPV/Prunus interactions.

Flu researchers slam US agency for hoarding data

Better sharing of information would help vaccine design.

Avian Influenza Virus H5N1: A Review of Its History and Information Regarding Its Potential to Cause the Next Pandemic

Avian influenza virus H5N1, which has been limited to poultry, now has spread to migrating birds and has emerged in mammals and among the human population. It presents a distinct threat of a pandemic for which the World Health Organization and other organizations are making preparations. This article reviews information about the virus itself and its spread among poultry, migrating birds, mammals, and humans.

A severe acute respiratory syndrome-associated coronavirus-specific protein enhances virulence of an attenuated murine coronavirus

Most animal species that can be infected with the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) do not reproducibly develop clinical disease, hindering studies of pathogenesis. To develop an alternative system for the study of SARS-CoV, we introduced individual SARS-CoV genes (open reading frames [ORFs]) into the genome of an attenuated murine coronavirus. One protein, the product of SARS-CoV ORF6, converted a sublethal infection to a uniformly lethal encephalitis and enhanced virus growth in tissue culture cells, indicating that SARS-CoV proteins function in the context of a heterologous coronavirus infection. Furthermore, these results suggest that the attenuated murine coronavirus lacks a virulence gene residing in SARS-CoV. Recombinant murine coronaviruses cause a reproducible and well-characterized clinical disease, offer virtually no risk to laboratory personnel, and should be useful for elucidating the role of SARS-CoV nonstructural proteins in viral replication and pathogenesis.

Strategies for containing an emerging influenza pandemic in Southeast Asia

Highly pathogenic H5N1 influenza A viruses are now endemic in avian populations in Southeast Asia, and human cases continue to accumulate. Although currently incapable of sustained human-to-human transmission, H5N1 represents a serious pandemic threat owing to the risk of a mutation or reassortment generating a virus with increased transmissibility. Identifying public health interventions that might be able to halt a pandemic in its earliest stages is therefore a priority. Here we use a simulation model of influenza transmission in Southeast Asia to evaluate the potential effectiveness of targeted mass prophylactic use of antiviral drugs as a containment strategy. Other interventions aimed at reducing population contact rates are also examined as reinforcements to an antiviral-based containment policy. We show that elimination of a nascent pandemic may be feasible using a combination of geographically targeted prophylaxis and social distancing measures, if the basic reproduction number of the new virus is below 1.8. We predict that a stockpile of 3 million courses of antiviral drugs should be sufficient for elimination. Policy effectiveness depends critically on how quickly clinical cases are diagnosed and the speed with which antiviral drugs can be distributed.

Scrambling of the amino acids within the transmembrane domain of Vpu results in a simian-human immunodeficiency virus (SHIVTM) that is less pathogenic for pig-tailed macaques

Previous studies have shown that the transmembrane (TM) domain of the subtype B Vpu enhances virion release from cells and some studies have shown that this domain may form an oligomeric structure with properties of an ion channel. To date, no studies have been performed to assess the role of this domain in virus pathogenesis in a macaque model of disease. Using a pathogenic molecular clone of simian human immunodeficiency virus (SHIVKU-1bMC33), we have generated a novel virus in which the transmembrane domain of the Vpu protein was scrambled but maintained hydrophobic in nature (SHIVTM), which presumably would disrupt any ion channel TM properties of this protein. Vectors expressing the Vpu as a fusion protein with the enhanced green fluorescent protein (VpuTMEGFP) indicate that it was transported to the same intracellular compartment as the unmodified Vpu protein but did not down-regulate cell surface expression of CD4. To assess the pathogenicity of SHIVTM, three pig-tailed macaques were inoculated with the SHIVTM and monitored for 6-8 months for CD4+ T cell levels, viral loads and the stability of the sequence of the vpu gene. Our results indicated that unlike the parental SHIVKU-1bMC33, inoculation of macaques with SHIVTM did not cause a severe CD4+ T cell loss over the course of their infections. Sequence analysis of the vpu gene analyzed from sequential PBMC samples derived from macaques revealed that the scrambled TM was stable during the course of infection. At necropsy, examination of tissues revealed low viral loads and none of the pathology commonly observed in lymphoid and non-lymphoid tissues following inoculation with the pathogenic parental SHIVKU-1bMC33 virus. Thus, these results show for the first time that the TM domain of Vpu contributes to the pathogenicity of SHIVKU-1bMC33 in pig-tailed macaques.

Highly pathogenic H5N1 influenza virus infection in migratory birds

H5N1 avian influenza virus (AIV) has emerged as a pathogenic entity for a variety of species, including humans, in recent years. Here we report an outbreak among migratory birds on Lake Qinghaihu, China, in May and June 2005, in which more than a thousand birds were affected. Pancreatic necrosis and abnormal neurological symptoms were the major clinical features. Sequencing of the complete genomes of four H5N1 AIV strains revealed them to be reassortants related to a peregrine falcon isolate from Hong Kong and to have known highly pathogenic characteristics. Experimental animal infections reproduced typical highly pathogenic AIV infection symptoms and pathology.

Genetic determinants of cell type-specific poliovirus propagation in HEK 293 cells

The ability of poliovirus to propagate in neuronal cells can be reduced by introducing appropriate nucleotide substitutions into the viral genome. Specific mutations scattered throughout the poliovirus genome yielded the live attenuated vaccine strains of poliovirus. Neuron-specific propagation deficits of the Sabin strains are partially encrypted within a confined region of the internal ribosomal entry site (IRES), which carries attenuating point mutations in all three serotypes. Recently, high levels of neurovirulence attenuation were achieved with genetically engineered polioviruses containing heterologous IRES elements. This is exemplified with poliovirus recombinants replicating under control of a human rhinovirus type 2 (HRV2) IRES element. We have carried out experiments delineating the genetic basis for neuronal IRES function. Neuronal dysfunction of the HRV2 IRES is determined mainly by IRES stem-loop domain V, the locus for attenuating point mutations within the Sabin strains. Neuronal incompetence associated with HRV2 IRES domain V is substantially more pronounced than that observed with the attenuating IRES point mutation of the Sabin serotype 1 vaccine strain. Mix-and-match recombination of polio and HRV2 IRES domain V suggests that the attenuation phenotype correlates with overall structural features rather than primary sequence. Our experiments have identified HEK 293 cells as a novel system for the study of neuron-specific replication phenotypes of poliovirus. This cell line, originally derived from embryonic human kidney, has recently been described to display neuronal characteristics. We report propagation properties in HEK 293 cells for poliovirus recombinants with attenuated neurovirulence in experimental animals that corroborate this observation.

Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost

Escape from specific T-cell responses contributes to the progression of human immunodeficiency virus type 1 (HIV-1) infection. T-cell escape viral variants are retained following HIV-1 transmission between major histocompatibility complex (MHC)-matched individuals. However, reversion to wild type can occur following transmission to MHC-mismatched hosts in the absence of cytotoxic T-lymphocyte (CTL) pressure, due to the reduced fitness of the escape mutant virus. We estimated both the strength of immune selection and the fitness cost of escape variants by studying the rates of T-cell escape and reversion in pigtail macaques. Near-complete replacement of wild-type with T-cell escape viral variants at an immunodominant simian immunodeficiency virus Gag epitope KP9 occurred rapidly (over 7 days) following infection of pigtail macaques with SHIVSF162P3. Another challenge virus, SHIVmn229, previously serially passaged through pigtail macaques, contained a KP9 escape mutation in 40/44 clones sequenced from the challenge stock. When six KP9-responding animals were infected with this virus, the escape mutation was maintained. By contrast, in animals not responding to KP9, rapid reversion of the K165R mutation occurred over 2 weeks after infection. The rapidity of reversion to the wild-type sequence suggests a significant fitness cost of the T-cell escape mutant. Quantifying both the selection pressure exerted by CTL and the fitness costs of escape mutation has important implications for the development of CTL-based vaccine strategies.

Pathogenesis of Hong Kong H5N1 influenza virus NS gene reassortants in mice: the role of cytokines and B- and T-cell responses

The severity of disease caused in humans by H5N1 influenza viruses remains unexplained. The NS gene of Hong Kong H5N1/97 viruses was shown to contribute to high pathogenicity of reassortants in a pig model. However, the molecular pathogenesis and host immune response underlying this phenomenon remain unclear. Here, in a mouse model, H1N1 A/Puerto Rico/8/34 (PR/8) reassortants that contained the H5N1/97 NS gene, the H5N1/01 NS gene, or an altered H5N1/97 NS gene encoding a Glu92→Asp substitution in NS1 was studied. The pathogenicity of reassortant viruses, the induction of cytokines and chemokine CXCL1 (KC) in the lungs and specific B- and T-cell responses was characterized. In mice infected with reassortant virus containing the H5N1/97 NS gene, the mouse lethal dose (50 %) and lung virus titres were similar to those of PR/8, which is highly pathogenic to mice. This reassortant virus required two more days than PR/8 to be cleared from the lungs of infected mice. Reassortants containing the altered H5N1/97 NS gene or the H5N1/01 NS gene demonstrated attenuated pathogenicity and lower lung titres in mice. Specific B- and T-cell responses were consistent with viral pathogenicity and did not explain the delayed clearance of the H5N1/97 NS reassortant. The reassortant induced elevated pulmonary concentrations of the inflammatory cytokines IL1α, IL1β, IL6, IFN-γand chemokine KC, and decreased concentrations of the anti-inflammatory cytokine IL10. This cytokine imbalance is reminiscent of the clinical findings in two humans who died of H5N1/97 infection and may explain the unusual severity of the disease.

Synthesis of reassortant infectious bursal disease virus in chickens injected directly with infectious clones from different virus strains

The infectious bursal disease virus (IBDV), a member of the Birnaviridae family, containing a bisegmented double-stranded RNA genome, encodes four structural viral proteins, VP1, VP2, VP3, and VP4, as well as a non-structural protein, VP5. In the present paper, the segment A from two IBDV strains, field isolate ZJ2000 and attenuated strain HZ2, were inserted into one NaeI site by site-directed silent mutagenesis and subcloned into the eukaryotic expression plasmid pCI under the control of the human cytomegalovirus (hCMV) immediate early enhancer and promoter to construct the recombinant plasmids pCI-AKZJ2000 and pCI-AKHZ2, respectively. Each of the two recombinants was combined with another recombinant pCI plasmid containing the marked segment B of strain HZ2 (pCI-mB), and injected intramuscularly into non-immunized chickens. Two chimeric IBDV strains were recovered from the chickens. Two out of eight chickens in each of two groups showed the bursal histopathological change. The reassortant virus derived from pCI-AKZJ2000/pCI-mB can infect chicken embryos and shows relatively low virulence. We have developed a novel virus reverse genetic approach for the study of IBDV. The results also form the basis for investigating the role of VP1 in viral replication and pathogenecity.