Virology Journal - Latest articles

Migratory birds, the H5N1 influenza virus and the scientific method

Thomas P Weber and Nikolaos I Stilianakis — 2008-05-09

Background: The role of migratory birds and of poultry trade in the dispersal of highly pathogenic H5N1 is still the topic of intense and controversial debate. In a recent contribution to this journal, Flint argues that the strict application of the scientific method can help to resolve this issue.DiscussionWe argue that Flint's identification of the scientific method with null hypothesis testing is misleading and counterproductive. There is far more to science than the testing of hypotheses; not only the justification, but also the discovery of hypotheses belong to science. We also show why null hypothesis testing is weak and that Bayesian methods are a preferable approach to statistical inference. Furthermore, we criticize the analogy put forward by Flint between involuntary transport of poultry and long-distance migration.SummaryTo expect ultimate answers and unequivocal policy guidance from null hypothesis testing puts unrealistic expectations on a flawed approach to statistical inference and on science in general.

Closing two doors of viral entry: Intramolecular combination of a coreceptor- and fusion inhibitor of HIV-1

2008-05-01

We describe a novel strategy in which two inhibitors of HIV viral entry were incorporated into a single molecule. This bifunctional fusion inhibitor consists of an antibody blocking the binding of HIV to its co-receptor CCR5, and a covalently linked peptide which blocks envelope mediated virus-cell fusion. This novel bifunctional molecule is highly active on CCR5- and X4-tropic viruses in a single cycle assay and a reporter cell line with IC50 values of 0.03-0.05 nM. We demonstrated that both inhibitors contribute to the antiviral activity. In the natural host peripheral blood mononuclear cells (PBMC) the inhibition of CXCR4-tropic viruses is dependant on the co-expression of CCR5 and CXCR4 receptors. This bifunctional inhibitor may offer potential for improved pharmacokinetic parameters for a fusion inhibitor in humans and the combination of two active antiviral agents in one molecule may provide better durability in controlling the emergence of resistant viruses.

Genetic diversity and silencing suppression effects of Rice yellow mottle virus and the P1 protein

Christelle Sire, Martine Bangratz-Reyser, Denis Fargette and Christophe Brugidou — 2008-04-30

Background: PTGS (post-transcriptional gene silencing) is used to counter pathogenic invasions, particularly viruses. In return, many plant viruses produce proteins which suppress silencing directed against their RNA. The diversity of silencing suppression at the species level in natural hosts is unknown. Results: We investigated the functional diversity of silencing suppression among isolates of the African RYMV (Rice yellow mottle virus) in rice. The RYMV-P1 protein is responsible for cell-to-cell movement and is a silencing suppressor. Transgenic gus-silencing rice lines were used to investigate intra-specific and serogroup silencing suppression diversity at two different levels: that of the virion and the P1 silencing suppressor protein. Our data provide evidence that silencing suppression is a universal phenomenon for RYMV species. However, we found considerable diversity in their ability to suppress silencing which was not linked to RYMV phylogeny, or pathogenicity. At the level of the silencing suppressor P1 alone, we found similar results to those previously found at the virion level. In addition, we showed that cell-to-cell movement of P1 was crucial for the efficiency of silencing suppression. Mutagenesis of P1 demonstrated a strong link between some amino acids and silencing suppression features with, one on the hand, the conserved amino acids C95 and C64 involved in cell-to-cell movement and the strength of suppression, respectively, and on the other hand, the non conserved F88 was involved in the strength of silencing suppression. Conclusions: We demonstrated that intra-species diversity of silencing suppression is highly variable and by mutagenesis of P1 we established the first link between silencing suppression and genetic diversity. These results are potentially important for understanding virus-host interactions.

Varicella-zoster virus ORF 58 gene is dispensable for viral replication in cell culture

2008-04-30

Background: Open reading frame 58 (ORF58) of varicella-zoster virus (VZV) lies at the 3'end of the Unique long (UL) region and its functional is unknown. In order to clarify whether ORF58 is essential for the growth of VZV, we constructed a deletion mutant of ORF58 (pOka-BACdelta58) from the Oka parental genome cloned into a bacterial artificial chromosome (pOka-BAC). Results: The ORF58-deleted virus (rpOkadelta58) was reconstituted from the pOka-BAC[increment]58 genome in MRC-5 cells, indicating that the ORF58 gene is non-essential for virus growth. Comparison of the growth rate of rpOkadelta58 and recombinant wild-type virus by assessing plaque sizes revealed no significant differences between them both in MRC-5cells and malignant melanoma cells. Conclusions: This study shows that the ORF58 gene is dispensable for viral replication and does not affect the virus' ability to form plaques in vitro.

Epidemiology of foot-and-mouth disease in Landhi Dairy Colony, Pakistan, the world largest Buffalo colony

Joern Klein, Manzoor Hussain, Munir Ahmad, Muhammad Afzal and Soren Alexandersen — 2008-04-29

Background: Foot-and-mouth disease (FMD) is endemic in Pakistan and causes huge economic losses. This work focus on the Landhi Dairy Colony (LDC), located in the suburbs of Karachi. LDC is the largest Buffalo colony in the world, with more than 300,000 animals (around 95 % buffaloes and 5 % cattle, as well as an unknown number of sheep and goats). Each month from April 2006 to April 2007 we collected mouth-swabs from apparently healthy buffaloes and cattle, applying a convenient sampling based on a two-stage random sampling scheme, in conjunction with participatory information from each selected farm. Furthermore, we also collected epithelium samples from animals with clinical disease, as well as mouth-swabs samples from those farms. In addition, we analysed a total of 180 serum samples randomly collecting 30 samples each month at the local slaughterhouse, from October 2006 to March 2007. Samples have been screened for FMDV by real-time RT-PCR and the partial or full 1D coding region of selected isolates has been sequenced. Serum samples have been analysed by applying serotype-specific antibody ELISA and non-structural proteins (NSP) antibody ELISA. Results: FMDV infection prevalence at aggregate level shows an endemic occurrence of FMDV in the colony, with peaks in August 2006, December 2006 and February 2007 to March 2007. A significant association of prevalence peaks to the rainy seasons, which includes the coldest time of the year and the muslimic Eid-festival, has been demonstrated. Participatory information indicated that 88 % of all questioned farmers vaccinate their animals. Analysis of the serum samples showed high levels of antibodies for serotypes O, A, Asia 1 and C. The median endpoint-titre for all tested serotypes, except serotype C, in VNT titration is at a serum dilution of equal or above 1/100. All 180 serum samples collected have been tested for antibodies against the non-structural proteins and all but four have been found positive. Out of the 106 swab-samples from apparently healthy and affected animals positive in real-time RT-PCR, we sequenced the partial or full 1D coding region from 58 samples. In addition we sequenced the full 1D coding region of 17 epithelium samples from animals with clinical signs of FMD. From all sequenced samples, swabs and epithelium, 19 belong to the regional PanAsia II lineage of serotype O and 56 to the A/Iran/2005 lineage of serotype A. Conclusions: For an effective and realisable FMD control program in LDC, we suggest to introduce a twice annually mass vaccination of all buffaloes and cattle in the colony. These mass vaccinations should optimally take place shortly before the beginning of the two rainy periods, e.g. in June and September. Those vaccinations should, in our opinion, be in addition to the already individually performed vaccinations of single animals, as the latter usually targets only newly introduced animals. This suggested combination of mass vaccination of all large ruminants with the already performed individually vaccination should provide a continuous high level of herd immunity in the entire colony. Vaccines used for this purpose should contain the matching vaccine strains, i.e. as our results indicate antigens for A/Iran/2005 and the regional type of serotype O (PanAsia II), but also antigens of the, in this world region endemic, Asia 1 lineage should be included. In the long term it will be important to control the vaccine use, so that subclinical FMD will be avoided.

Effect of influenza and pneumococcal vaccines in elderly persons in years of low influenza activity

Brith Christenson, Karlis Pauksen and Staffan P.E. Sylvan — 2008-04-28

Background: The present prospective study was conducted from 2003-2005, among all individuals 65 years and older in Uppsala County, a region with 300 000 inhabitants situated close to the Stockholm urban area. The objective of this study was to assess the preventive effect of influenza and pneumococcal vaccination in reducing hospitalisation and length of hospital stay (LOHS) even during periods of low influenza activity. The specificity of the apparent vaccine associations were evaluated in relation to the influenza seasons. Results: In 2003, the total study population was 41,059, of which 12,907 (31%) received influenza vaccine of these, 4,447 (11%) were administered the pneumococcal vaccine. In 2004, 14,799 (34%) individuals received the influenza vaccine and 8,843 (21%) the pneumococcal vaccine and in 2005 16,926 (39%) individuals were given the influenza vaccine and 12,340 (28%) the pneumococcal vaccine. Our findings indicated that 35 % of the vaccinated cohort belonged to a medical risk category (mainly those persons that received the pneumococcal vaccine). Data on hospitalisation and mortality during the 3-year period were obtained from the administrative database of the Uppsala county council During the influenza seasons, reduction of hospital admissions and significantly shorter in-hospital stay for influenza was observed in the vaccinated cohort (below 80 years of age). For individuals who also had received the pneumococcal vaccine, a significant reduction of hospital admissions and of in-hospital stay was observed for invasive pneumococcal disease and for pneumococcal pneumonia. Effectiveness was observed for cardiac failure even in persons that also had received the pneumococcal vaccine, despite that the pneumococcal vaccinated mainly belonged to a medical risk category. Reduction of death from all causes was observed during the influenza season of 2004, in the 75-84-year old age group and in all age-groups during the influenza season 2005. Conclusions: The present study confirmed the additive effect of the two vaccines in the elderly, which was associated with a reduced risk in hospitalisation and a reduction in mean LOHS in seasons with low influenza activity.

Use of a commercial enzyme immunoassay to monitor dengue virus replication in cultured cells

Juan E Ludert, Clemente Mosso, Ivonne Ceballos-Olvera and Rosa M del Angel — 2008-04-25

Current methods for dengue virus quantitation are either time consuming, technically demanding or costly. As an alternative, the commercial enzyme immunoassay PlateliaTM Dengue NS1 AG (Bio-Rad Laboratories) was used to monitor semiquantitatively dengue virus replication in cultured cells. The presence of NS1 protein was evaluated in supernatants from Vero and C6/36 cells infected with dengue virus. The amount of NS1 detected in the supernatants of infected cells was proportional to the initial MOI used and to the time of post infection harvest. This immunoassay was also able to detect the presence of NS1 in the supernatants of infected human macrophages. Inhibition of dengue virus replication in C6/36 cells treated with lysosomotropic drugs was readily monitored with the use of this assay. These results suggest that the PlateliaTM Dengue NS1 AG kit can be used as a fast and reliable surrogate method for the relative quantitation of dengue virus replication in cultured cells.

The herpesvirus 8 encoded chemokines vCCL2 (vMIP-II) and vCCL3 (vMIP-III) target the human but not the murine lymphotactin receptor

Hans R Lüttichau — 2008-04-21

Background: Large DNA-viruses such as herpesvirus and poxvirus encode proteins that target and exploit the chemokine system of their host. The Kaposi sarcoma- associated herpes virus (KSHV) encodes three chemokines. Two of these, vCCL2 and vCCL3, target the human lymphotactin receptor as an antagonist and a selective agonist, respectively. Therefore these virally endcoded chemokines have the potential to be used as tools in the study of lymphotactin receptor pathways in murine models. Results: The activities of vCCL2, vCCL3, human lymphotactin (XCL1) and murine lymphotactin (mXCL1) were probed in parallel on the human and murine lymphotactin receptor (XCR1 and mXCR1) using a phosphatidyl-inositol assay. On the human XCR1, vCCL3, mXCL1 and XCL1 acted as agonists. In contrast, only mXCL1 was able to activate the murine lymphotactin receptor. Using the same assay, vCCL2 was able to block the response using any of the three agonists on the humane lymphotactin receptor with IC50s of 2–3 nM. However, vCCL2 was unable to block the response of mXCL1 through the murine lymphotactin receptor. Conclusion: This study shows that vCCL2 and vCCL3 cannot be used to investigate lymphotactin receptor pathways in murine models. These results also add vCCL2 and vCCL3 to a growing list of viral chemokines with known human chemokine receptor targets, which do not target the corresponding murine receptors. This fits with the observation that viral and endogenous ligands for the same human chemokine receptor tend to have relatively divergent amino-acid sequences, suggesting that these viruses have fine-tuned the design of their chemokines such that the action of the viral encoded chemokines cannot be expected to cross species barriers.

Changes in viral load and HBsAg and HBeAg status with age in HBV chronic carriers in The Gambia

2008-04-16

Background: Little is known about changes in hepatitis B viral load (HBV DNA) in relation to age in Africa. The aim of this study is to determine the natural course of HBV chronic infection, particularly in relation to sequential changes in serum HBV DNA levels and hepatitis B surface (HBsAg) antigen/hepatitis e antigen (HBeAg) status by age. Methods: The study was conducted on 190 HBV chronic carriers, aged 1–19 years who were followed for 19 years. 160, 99 and 123 were traced at 5, 9 and 19 years later. All available samples were tested for HBsAg and HBeAg, whilst 170, 61, 63 and 81 were tested for HBV DNA at the baseline, and at 5, 9 and 19 years following recruitment. Results: In general HBeAg which correlated with high levels of HBV DNA was lost at a much faster rate than HBsAg. 86% of the carriers who were recruited at the age of 1–4 yrs lost HBeAg by the age of 19 years compared to 30% who lost HBsAg. HBeAg negative carriers had serum HBV DNA levels of < 105 copies per mL, HBV DNA positivity declined from 100% in 1–4 yrs old carriers at recruitment to 62.5%,60% and 88% at 5, 9 and 19 years respectively following recruitment. Conclusion: After 19 years of follow up, the majority of HBV surface antigen carriers had lost HBeAg positivity and had low levels of viral replication. However small proportions (10–20%) retained HBeAg and continue to have high levels of viral replication.

Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

Andrew E Firth — 2008-04-14

Background: The genus Orbivirus includes several species that infect livestock – including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic. Results: Bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the Orbivirus genome segment 9, overlapping the VP6 cistron in the +1 reading frame. In BTV, a 77–79 codon AUG-initiated open reading frame (hereafter ORFX) is present in all 48 segment 9 sequences analysed. The pattern of base variations across the 48-sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP6 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP6. The ORFX AUG codon has a strong Kozak context in all 48 sequences. Each has only one or two upstream AUG codons, always in the VP6 reading frame, and (with a single exception) always with weak or medium Kozak context. Thus, in BTV, ORFX may be translated via leaky scanning. A long (83–169 codon) ORF is present in a corresponding location and reading frame in all other Orbivirus species analysed except Saint Croix River virus (SCRV; the most divergent). Again, the pattern of base variations across sequence alignments indicates multiple coding in the VP6 and ORFX reading frames. Conclusion: At ~9.5 kDa, the putative ORFX product in BTV is too small to appear on most published protein gels. Nonetheless, a review of past literature reveals a number of possible detections. We hope that presentation of this bioinformatic analysis will stimulate an attempt to experimentally verify the expression and functional role of ORFX, and hence lead to a greater understanding of the molecular biology of these important pathogens.