New tools in nucleoside toolbox of tick-borne encephalitis virus reproduction inhibitors

Design and development of nucleoside analogs is an established strategy in the antiviral drug discovery field. Nevertheless, for many viruses the coverage of structure-activity relationships (SAR) in the nucleoside chemical space is not sufficient. Here we present the nucleoside SAR exploration for tick-borne encephalitis virus (TBEV), a member of Flavivirus genus. Promising antiviral activity may be achieved by introduction of large hydrophobic substituents in the position 6 of adenosine or bulky silyl groups to the position 5′. Introduction of methyls to the ribose moiety does not lead to inhibition of TBEV reproduction. Possible mechanisms of action of these nucleosides include the inhibition of viral entry or interaction with TBEV non-structural protein 5 methyltransferase or RNA-dependent RNA polymerase domains.     

Structural and functional analysis of methylation and 5'-RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5

The N-terminal 33 kDa domain of non-structural protein 5 (NS5) of dengue virus (DV), named NS5MTase(DV), is involved in two of four steps required for the formation of the viral mRNA cap (7Me)GpppA(2'OMe), the guanine-N7 and the adenosine-2'O methylation. Its S-adenosyl-l-methionine (AdoMet) dependent 2'O-methyltransferase (MTase) activity has been shown on capped (7Me+/-)GpppAC(n) RNAs. Here we report structural and binding studies using cap analogues and capped RNAs. We have solved five crystal structures at 1.8 A to 2.8 A resolution of NS5MTase(DV) in complex with cap analogues and the co-product of methylation S-adenosyl-l-homocysteine (AdoHcy). The cap analogues can adopt several conformations. The guanosine moiety of all cap analogues occupies a GTP-binding site identified earlier, indicating that GTP and cap share the same binding site. Accordingly, we show that binding of (7Me)GpppAC(4) and (7Me)GpppAC(5) RNAs is inhibited in the presence of GTP, (7Me)GTP and (7Me)GpppA but not by ATP. This particular position of the cap is in accordance with the 2'O-methylation step. A model was generated of a ternary 2'O-methylation complex of NS5MTase(DV), (7Me)GpppA and AdoMet. RNA-binding increased when (7Me+/-)GpppAGC(n-1) starting with the consensus sequence GpppAG, was used instead of (7Me+/-)GpppAC(n). In the NS5MTase(DV)-GpppA complex the cap analogue adopts a folded, stacked conformation uniquely possible when adenine is the first transcribed nucleotide at the 5' end of nascent RNA, as it is the case in all flaviviruses. This conformation cannot be a functional intermediate of methylation, since both the guanine-N7 and adenosine-2'O positions are too far away from AdoMet. We hypothesize that this conformation mimics the reaction product of a yet-to-be-demonstrated guanylyltransferase activity. A putative Flavivirus RNA capping pathway is proposed combining the different steps where the NS5MTase domain is involved.     

Changes in hematological and serum biochemical parameters in common marmosets (Callithrix jacchus) after inoculation with dengue virus

Background Marmosets are susceptible to dengue virus (DENV) infection. However, blood parameter data and clinical signs of DENV-infected marmosets are limited. Methods Blood hematological and serum biochemical values were obtained from twelve DENV-inoculated and four mock-infected marmosets. Additionally, body temperature and activity level were determined. Results Five DENV-inoculated marmosets demonstrated thrombocytopenia, nine demonstrated leucopenia, and five demonstrated an increase in the levels of AST, ALT, LDH, and BUN. Additionally, seven DENV-inoculated marmosets demonstrated clinical signs including fever and decreases in activity. None of the four mock-inoculated marmosets demonstrated changes in either hematological or biochemical parameters. Conclusions Marmosets inoculated with DENV exhibited clinical signs and changes in hematological and biochemical parameters. The results suggest that blood parameter data and clinical signs could potentially be useful markers for understanding the progress of DENV infection in studies using marmosets.     

Unique heparan sulfate from shrimp heads exhibits a strong inhibitory effect on infections by dengue virus and Japanese encephalitis virus

The structure and biological activities of a highly sulfated heparan sulfate (HS) extracted from shrimp (Penaeus brasiliensis) heads were characterized. Structurally the shrimp HS was more heterogenous than heparin, although it is still highly sulfated. The molecular mass of the shrimp HS preparation was determined to be 32.3 kDa by gel filtration HPLC. Analysis by surface plasmon resonance demonstrated that various growth/differentiation factors specifically bound to the shrimp HS with comparable affinity. Notably, the shrimp HS had a greater inhibitory effect against infections by dengue virus type 2 as well as Japanese encephalitis virus than heparin. Experiments on anticoagulant activity indicated that the shrimp HS exhibited significant anti-thrombin activity, but less than the commercial heparin. Hence, the HS preparation from shrimp heads, an industrial waste, is a prospective agent for a variety of clinical applications.     

Natural vertical transmission of dengue viruses in Aedes aegypti in selected sites in Cebu City,Philippines

We attempted to determine the vertical transmission of dengue virus (DENV) in Aedes aegypti in selected sites in Cebu City, Philippines. Mosquito sub‐adults were collected monthly from households and the field during the wet‐dry‐wet season from November, 2011 to July, 2012 and were laboratory‐reared to adults. Viral RNA extracts in mosquitoes were assayed by hemi‐nested RT‐PCR. Results showed that 62 (36.26%; n=679) out of 171 mosquito pools (n=2,871) were DENV+. The minimum infection rate (MIR) of DENV ranged from 0 in wet months to 48.22/1,000 mosquitoes in April, 2012 (mid‐dry). DENVs were detected in larvae, pupae, and male and female adults, with DENV‐4, DENV‐3, and DENV‐1, in that rank of prevalence. DENV‐1 co‐infected with either DENV‐3 or ?4 or with both in April, 2012; DENV‐3 and ?4 were present in both seasons. More DENV+ mosquitoes were collected from households than in field premises (p<0.001) and in the dry than in the wet season (p<0.05), with significant interaction (p<0.05) between sites and premises but no interaction between sites and seasons (p>0.05). By Generalized Linear Mixed models, the type of premises nested in sites and monthly total rainfall were significant predictors of monthly dengue cases (p<0.05) and not MIR, season, temperature, and relative humidity. Surveillance of DENV prevalence in Ae. aegypti and detecting their natural foci in the dry season provide an early warning signal of dengue outbreak.     

Progress towards understanding the pathogenesis of dengue hemorrhagic fever

Dengue virus (DENV) is a mosquito-borne virus belonging to the Flaviviridae family. There are 4 serotypes of DENV that cause human disease through transmission by mosquito vectors. DENV infection results in a broad spectrum of clinical symptoms, ranging from mild fever to dengue hemorrhagic fever (DHF), the latter of which can progress to dengue shock syndrome (DSS) and death. Researchers have made unremitting efforts over the last half-century to understand DHF pathogenesis. DHF is probably caused by multiple factors, such as virus-specific antibodies, viral antigens and host immune responses. This review summarizes the current progress of studies on DHF pathogenesis, which may provide important information for achieving effective control of dengue in the future.

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Graph hierarchies for phylogeography

Bayesian phylogeographic methods simultaneously integrate geographical and evolutionary modelling, and have demonstrated value in assessing spatial spread patterns of measurably evolving organisms. We improve on existing phylogeographic methods by combining information from multiple phylogeographic datasets in a hierarchical setting. Consider N exchangeable datasets or strata consisting of viral sequences and locations, each evolving along its own phylogenetic tree and according to a conditionally independent geographical process. At the hierarchical level, a random graph summarizes the overall dispersion process by informing which migration rates between sampling locations are likely to be relevant in the strata. This approach provides an efficient and improved framework for analysing inherently hierarchical datasets. We first examine the evolutionary history of multiple serotypes of dengue virus in the Americas to showcase our method. Additionally, we explore an application to intrahost HIV evolution across multiple patients.     

Distribution of three arbovirus antibodies among monkeys (Macaca fascicularis) in the Philippines

Serum samples from 54 monkeys were collected from healthy individuals in a monkey farm in Luzon island, Philippines, in 1999, and examined by IgM-capture ELISA and indirect IgG ELISA for the presence of dengue (DEN), Japanese encephalitis (JE) and chikungunya (CHIK) viruses. The positive rates for IgM ELISA were 3.7, 35.2 and 14.8% against DEN, JE and CHIK, respectively. Higher positive rates were obtained when indirect IgG ELISA was used: 100% against flaviviruses (JE or DEN) and 59.3% against CHIK virus. The results indicate a high prevalence of flavivirus infections such as JE and DEN, and a lesser prevalence of CHIK virus infections, among monkeys in the Philippines. These findings suggest possible sylvatic transmission cycles of these viruses.     

Study on the determinants of suckling mice neurovirulence of dengue 2 virus

Denguevirusescausedenguefever(DF),denguehaemorrhagicfever(DHF)anddengueshocksyndrome(DSS).DFisoneofthemostimportantarthropod-bornehumandiseasesintropicalandsubtropicalareas.Severallarge-scaledenguefeverepidemicsinSouthChinahavetakenplaceinSouthChinaeveryfewyearssince1978andmorethan1000casesofdenguefeverwerereportedinFuzhouofChinainAugust1999[1].However,nodenguevaccinesarecommerciallyavailableatpresent.Onemajordifficultyhinderingthedevelopmentofadenguevaccinehasbeenthelackofasuitableanim…