Co-distribution and co-infection of chikungunya and dengue viruses

BACKGROUND Chikungunya and dengue infections are spatio-temporally related. The current review aims to determine the geographic limits of chikungunya, dengue and the principal mosquito vectors for both viruses and to synthesise current epidemiological understanding of their co-distribution. METHODS Three biomedical databases (PubMed, Scopus and Web of Science) were searched from their inception until May 2015 for studies that reported concurrent detection of chikungunya and dengue viruses in the same patient. Additionally, data from WHO, CDC and Healthmap alerts were extracted to create up-to-date global distribution maps for both dengue and chikungunya. RESULTS Evidence for chikungunya-dengue co-infection has been found in Angola, Gabon, India, Madagascar, Malaysia, Myanmar, Nigeria, Saint Martin, Singapore, Sri Lanka, Tanzania, Thailand and Yemen; these constitute only 13 out of the 98 countries/territories where both chikungunya and dengue epidemic/endemic transmission have been reported. CONCLUSIONS Understanding the true extent of chikungunya-dengue co-infection is hampered by current diagnosis largely based on their similar symptoms. Heightened awareness of chikungunya among the public and public health practitioners in the advent of the ongoing outbreak in the Americas can be expected to improve diagnostic rigour. Maps generated from the newly compiled lists of the geographic distribution of both pathogens and vectors represent the current geographical limits of chikungunya and dengue, as well as the countries/territories at risk of future incursion by both viruses. These describe regions of co-endemicity in which lab-based diagnosis of suspected cases is of higher priority.

Prevalence, codetection and seasonal distribution of upper airway viruses and bacteria in children with acute respiratory illnesses with cough as a symptom

Most studies exploring the role of upper airway viruses and bacteria in paediatric acute respiratory infections (ARI) focus on specific clinicaldiagnoses and/or do not account for virus–bacteria interactions. We aimed to describe the frequency and predictors of virus and bacteria codetection in children with ARI and cough, irrespective of clinical diagnosis. Bilateral nasal swabs, demographic, clinical and risk factor data were collected at enrollment in children aged <15 years presenting to an emergency department with an ARI and where cough was a symptom. Swabs were tested by polymerase chain reaction for 17 respiratory viruses and seven respiratory bacteria. Logistic regression was used to investigate associations between child characteristics and codetection of the organisms of interest. Between December 2011 and August 2014, swabs were collected from 817 (93.3%) of 876 enrolled children, median age 27.7 months (interquartile range13.9–60.3 months). Overall, 740 (90.6%) of 817 specimens were positive for any organism. Both viruses and bacteria were detected in 423 specimens (51.8%). Factors associated with codetection were age (adjusted odds ratio (aOR) for age <12 months = 4.9, 95% confidence interval (CI) 3.0, 7.9; age 12 to <24 months = 6.0, 95% CI 3.7, 9.8; age 24 to <60 months = 2.4, 95% CI 1.5, 3.9), male gender (aOR 1.46; 95% CI 1.1, 2.0), child care attendance (aOR 2.0; 95% CI 1.4, 2.8) and winter enrollment (aOR 2.0; 95% CI 1.3, 3.0). Haemophilus influenzae dominated the virus–bacteria pairs. Virus–H. influenzae interactions in ARI should be investigated further, especially as the contribution of nontypeable H. influenzae to acute and chronic respiratory diseases is being increasingly recognized.

The biology and pathogenesis of hepatitis viruses

Viral hepatitis is caused mainly by infection with one of the five hepatitis viruses, which use the liver as their primary site of replication. Each of these, known as hepatitis A through E viruses (HAV to HEV), belong to different virus families, have unique morphology, genomic organization and replication strategy. These viruses cause similar clinical manifestations during the acute phase of infection but vary in their ability to cause chronic infection. While HAV and HEV cause only acute disease with no chronic sequelae, HBV, HCV and HDV cause varying degrees of chronicity and liver injury, which can progress to cirrhosis and liver cancers. Though specific serological tests are available for the known hepatitis viruses, nearly 20% of all hepatitis cases show no markers. Antiviral therapy is also recommended for some hepatitis viruses and a preventive vaccine is available only for hepatitis B. More research and public awareness programmes are needed to control the disease. This review will provide an overview of the hepatitis viruses and the disease they cause.

Non-segmented negative sense RNA viruses as vectors for vaccine development

This article intends to cover two aspects of non-segmented negative sense RNA viruses. In the initial section, the strategy employed by these viruses to replicate their genomes is discussed. This would help in understanding the later section in which the use of these viruses as vaccine vectors has been discussed. For the description of the replication strategy which encompasses virus genome transcription and genome replication carried out by the same RNA dependent RNA polymerase complex, a member of the prototype rhabdovirus family - Chandipura virus has been chosen as an example to illustrate the complex nature of the two processes and their regulation. In the discussion on these viruses serving as vectors for carrying vaccine antigen genes, emphasis has been laid on describing the progress made in using the attenuated viruses as vectors and a description of the systems in which the efficiency of immune responses has been tested.

Differentiation of rinderpest and peste des petits ruminants viruses using specific cDNA clones

The morbilliviruses which infect ruminants, rinderpest (RPV) and peste des petits ruminants (PPRV), are difficult to distinguish serologically. They can be distinguished by differential neutralisation tests and by the migration of the major virus structural protein, the nucleocapsid protein, on polyacrylamide gels. Both these methods are time consuming and require the isolation of live virus for identification; they are not suitable for analysis of material directly from post-mortem specimens. We describe a rapid method for differential diagnosis of infections caused by RPV or PPRV, which uses specific cDNA probes, derived from the mRNAs for the nucleocapsid protein of each virus, which can be used to distinguish unequivocally the two virus types rapidly.

Artificial Bee Colony (ABC) for multi-objective design optimization of composite structures

In this paper, we present a generic method/model for multi-objective design optimization of laminated composite components, based on Vector Evaluated Artificial Bee Colony (VEABC) algorithm. VEABC is a parallel vector evaluated type, swarm intelligence multi-objective variant of the Artificial Bee Colony algorithm (ABC). In the current work a modified version of VEABC algorithm for discrete variables has been developed and implemented successfully for the multi-objective design optimization of composites. The problem is formulated with multiple objectives of minimizing weight and the total cost of the composite component to achieve a specified strength. The primary optimization variables are the number of layers, its stacking sequence (the orientation of the layers) and thickness of each layer. The classical lamination theory is utilized to determine the stresses in the component and the design is evaluated based on three failure criteria: failure mechanism based failure criteria, maximum stress failure criteria and the tsai-wu failure criteria. The optimization method is validated for a number of different loading configurations-uniaxial, biaxial and bending loads. The design optimization has been carried for both variable stacking sequences, as well fixed standard stacking schemes and a comparative study of the different design configurations evolved has been presented. Finally the performance is evaluated in comparison with other nature inspired techniques which includes Particle Swarm Optimization (PSO), Artificial Immune System (AIS) and Genetic Algorithm (GA). The performance of ABC is at par with that of PSO, AIS and GA for all the loading configurations. (C) 2009 Elsevier B.V. All rights reserved.

Structure-function relationships of icosahedral plant viruses

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary morganization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

A model for heat transfer in a honey bee swarm

A swarm is a temporary structure formed when several thousand honey bees leave their hive and settle on some object such as the branch of a tree. They remain in this position until a suitable site for a new home is located by the scout bees. A continuum model based on heat conduction and heat generation is used to predict temperature profiles in swarms. Since internal convection is neglected, the model is applicable only at low values of the ambient temperature T-a. Guided by the experimental observations of Heinrich (1981a-c, J. Exp. Biol. 91, 25-55; Science 212, 565-566; Sci. Am. 244, 147-160), the analysis is carried out mainly for non-spherical swarms. The effective thermal conductivity is estimated using the data of Heinrich (1981a, J. Exp. Biol. 91, 25-55) for dead bees. For T-a = 5 and 9 degrees C, results based on a modified version of the heat generation function due to Southwick (1991, The Behaviour and Physiology of Bees, PP 28-47. C.A.B. International, London) are in reasonable agreement with measurements. Results obtained with the heat generation function of Myerscough (1993, J. Theor. Biol. 162, 381-393) are qualitatively similar to those obtained with Southwick's function, but the error is more in the former case. The results suggest that the bees near the periphery generate more heat than those near the core, in accord with the conjecture of Heinrich (1981c, Sci. Am. 244, 147-160). On the other hand, for T-a = 5 degrees C, the heat generation function of Omholt and Lonvik (1986, J. Theor. Biol. 120, 447-456) leads to a trivial steady state where the entire swarm is at the ambient temperature. Therefore an acceptable heat generation function must result in a steady state which is both non-trivial and stable with respect to small perturbations. Omholt and Lonvik's function satisfies the first requirement, but not the second. For T-a = 15 degrees C, there is a considerable difference between predicted and measured values, probably due to the neglect of internal convection in the model.

Monoclonal antibodies in the study of architecture of plant viruses

Monoclonal antibodies have been used as probes to study the architecture of several plant viruses over the past decade. These studies complement the information obtained through X-ray crystallography and help in delineating epitopes on the surface of the virus. The monoclonal antibodies that recognize distinct epitopes also aid in unravelling the mechanisms of assembly/disassembly of virus particles. Group-specific and strain-specific monoclonal antibodies are widely used in the classification of viruses. The significant developments made in this emerging area are reviewed here with specific examples.

A new parasitic bee of the genus Braunsapis from India (Hymenoptera : Apidae : Allodapini)

A new species of allodapine bee (Apidae, Xylocopinae, Allodapini), Braunsapis bislensis, is described from southern India. To judge by its reduced mouthparts and scopa, it is a social parasite, perhaps in nests of B. puangensis (Cockerell).

Viruses and viral proteins

For more than 30 years X-ray crystallography has been by far the most powerful approach for determining the structures of viruses and viral proteins at atomic resolution. The information provided by these structures, which covers many important aspects of the viral life cycle such as cell-receptor recognition, viral entry, nucleic acid transfer and genome replication, has extensively enriched our vision of the virus world. Many of the structures available correspond to potential targets for antiviral drugs against important human pathogens. This article provides an overview of the current knowledge of different structural aspects of the above-mentioned processes.

Modeling the co-transport of viruses and colloids in unsaturated porous media

A mathematical model is developed to simulate the co-transport of viruses and colloids in unsaturated porous media under steady-state flow conditions. The virus attachment to the mobile and immobile colloids is described using a linear reversible kinetic model. Colloid transport is assumed to be decoupled from virus transport; that is, we assume that colloids are not affected by the presence of attached viruses on their surface. The governing equations,are solved numerically using an alternating three-step operator splitting approach. The model is verified by fitting three sets of experimental data published in the literature: (1) Syngouna and Chrysikopoulos (2013) and (2) Walshe et al. (2010), both on the co-transport of viruses and clay colloids under saturated conditions, and (3) Syngouna and Cluysikopoulos (2015) for the co-transport of viruses and clay colloids under unsaturated conditions. We found a good agreement between observed and fitted breakthrough curves (BTCs) under both saturated and unsaturated conditions. Then, the developed model was used to simulate the co-transport of viruses and colloids in porous media under unsaturated conditions, with the aim of understanding the relative importance of various processes on the co-transport of viruses and colloids in unsaturated porous media. The virus retention in porous media in the presence of colloids is greater during unsaturated conditions as compared to the saturated conditions due to: (1) virus attachment to the air-water interface (AWI), and (2) co-deposition of colloids with attached viruses on its surface to the AWL A sensitivity analysis of the model to various parameters showed that the virus attachment to AWI is the most sensitive parameter affecting the BTCs of both free viruses and total mobile viruses and has a significant effect on all parts of the BTC. The free and the total mobile viruses BTCs are mainly influenced by parameters describing virus attachment to the AIM, virus interaction with mobile and immobile colloids, virus attachment to solid-water interface (SWI), and colloid interaction with SWI and AWL The virus BTC is relatively insensitive to parameters describing the maximum adsorption capacity of the AWI for colloids, inlet colloid concentration, virus detachment rate coefficient from the SW!, maximum adsorption capacity of the AWI for viruses and inlet virus concentration. (C) 2015 Elsevier B.V. All rights reserved.