SEROPREVALENCE OF INFECTIOUS BOVINE RHINOTRACHEITIS (IBR) IN NORTH EASTERN (NE) STATES OF INDIA

Infectious bovine rhinotracheitis (IBR) is an infectious disease caused by BoHV-1 and belongs to the Herpesviridae family. IBR is endemic in India including north eastern states of the country. Hence the study was undertaken to understand the seroprevalence of IBR in north eastern parts of the country. A total of 3125 cattle (Holstein Friesian crossbred) serum samples from 35 districts of five north eastern states (Assam, Manipur, Meghalaya, Mizoram, and Sikkim) of India were screened for infectious bovine rhinotracheitis (IBR) virus antibodies using Avidin biotin ELISA.  A two-stage random sampling methodology was followed for the collection of samples. Results from the present study revealed that the overall seropositivity was reported around 29.50% while the highest and lowest seropositivity of 43.39% and 16.66% were reported in the states of Sikkim and Assam respectively, followed by Mizoram (42.16%), Manipur (29.86%) and Meghalaya (27.40%). Cattle of higher age groups showed the highest seropositivity compared to younger ones. A higher percent of IBR antibodies in cattle of NE states is a cause of concern and a detailed study on IBR prevalence comprising of a large number of the bovine population need to be undertaken

Artificial intelligence and Machine Learning based Techniques in Analyzing the COVID-19 Gene Expression data: A Review

The novel Coronavirus associated with respiratory illness has become a new threat to human health as it is spreading very rapidly among the human population. Scientists and healthcare specialists throughout the world are still looking for a breakthrough technology to help combat the Covid-19 outbreak, despite the recent worldwide urgency. The use of Machine Learning (ML) and Artificial Intelligence (AI) in earlier epidemics has encouraged researchers by providing a fresh approach to combating the latest Coronavirus pandemic. This paper aims to comprehensively review the role of AI and ML for analysis of gene expressed data of COVID-1

Sheep Associated-Malignant Catarrhal Fever: Past, present, and future

Members of Artiodactyla can contract the infectious disease Malignant Catarrhal Fever (MCF), which has a wide range of symptoms. Ten known viruses contribute to the disease, the two most significant ones being Ovine gamma herpes virus 2 (OvHV-2) and Alcelaphine gamma herpes virus 1 (AIHV-1). In the African subcontinent, AIHV-1 is seen in most MCF cases. In the Indian scenario, Ovine gamma herpes virus-2 is the main culprit. MCF is reported in certain pockets of India. Its threat to wildlife is not yet completely understood. In AIHV-1, wildebeests serve as the primary MCF reservoir, whereas with OvHV-2, the primary MCF reservoir is sheep. In India, OvHV-2 causes MCF in deer species, bison, and water buffaloe. The life cycle and properties of this virus are not yet wholly deciphered. To understand the impact of the disease and the threat it may pose in the future, we need to have diagnostic techniques in place. Currently, PCR is the most commonly used diagnostic technique. Work should be done on field-oriented tests like ELISA and LFA, which are helpful in areas without sophisticated lab facilities. Treatment protocols must be in place, as culling bovines is not an accepted policy in India. Probable plans for overcoming all these problems are discussed in this article

QUASISPECIES FEATURE IN SARS-CoV-2

Since the identification of the SARS-CoV-2, genus Beta- Coronavirus, in January 2020, the virus quickly spread in less than 3 months to all continents with a susceptible human population of about a 7.9billion, and still in active circulation. In the process, it has accumulated mutations leading to genetic diversity. Regular emergence of variants of concern/significance in different ecology shows genetic heterogeneity in the base population of SARS-CoV-2 that is continuously expanding with the passage of the virus in the vast susceptible human population. Natural selection of mutant occurs frequently in a positive sense (+) single-stranded (ss) RNA virus upon replication in the host.  The Pressure of sub-optimal levels of virus-neutralizing antibodies and also innate immunity influence the process of genetic/ antigenic selection. The fittest of the mutants, that could be more than one, propagate and emerge as variants. The existence of different lineages, clades, and strains, as well as genetic heterogeneity of plaque purified virus population, justifies SARS-CoV-2 as ‘Quasispecies’ that refers to swarms of mutant sequences generated during replication of the viral genome, and all mutant sequences may not lead to virion. Viruses having a quasispecies nature may end up with progressive antigenic changes leading to antigenic plurality that is driven by ecology, and this phenomenon challenges vaccination-based control programs

COVID-19 PANDEMIC: A SYSTEMATIC REVIEW ON THE CORONAVIRUSES OF ANIMALS AND SARS-CoV-2

Coronaviruses (CoVs), classified into four genera, viz., alpha-, beta-, gamma-, and Delta- CoV, represent an important group of diverse transboundary pathogens that can infect a variety of mammalian and avian species including humans, animals, poultry, and non-poultry birds. CoVs primarily infect lung and gut epithelial cells, besides monocytes and macrophages. CoVs have high mutation rates causing changes in host specificity, tissue tropism, and mode of virus excretion and transmissions. The recent CoV zoonoses are SARS, MERS, and COVID-19 that are caused by the transmission of beta-CoVs of bats to humans.  Recently, reverse zoonoses of the COVID-19 virus have been detected in dogs, tigers, and minks. Beta-CoV strains also infect bovine (BCoV) and canine species (CRCoV); both these beta-CoVs might have originated from a common ancestor. Despite the high genetic similarity between BCoV, CRCoV, and HCoV-OC43, these differ in species specificity. Alpha-CoV strains infect canine (CCoV), feline (FIPV), swine (TGEV and PEDV), and humans (HCoV229E and NL63). Six coronavirus species are known to infect and cause disease in pigs, seven in human beings, and two in dogs. The high mutation rate in CoVs is attributed to error-prone 3′-5′ exoribonuclease (NSP 14), and genetic recombination to template shift by the polymerase. The present compilation describes the important features of the CoVs and diseases caused in humans, animals, and birds that are essential in surveillance of diverse pool of CoVs circulating in nature, and monitoring interspecies transmission, zoonoses, and reverse zoonoses

Research Article A new Informatics Framework for Evaluating the Codon Usage Metrics, Evolutionary Models and Phylogeographic reconstruction of Tomato yellow leaf curl virus (TYLCV) in different regions of Asian countries

Tomato yellow leaf curl virus (TYLCV) is a major devastating viral disease, majorly affecting the tomato production globally. The disease is majorly transmitted by the Whitefly. The Begomovirus (TYLCV) having a six major protein coding genes, among them the C1/AC1 is evidently associated with viral replication. Owing to immense role of C1/AC1 gene, the present study is an initial effort to elucidate the factors shaping the codon usage bias and evolutionary pattern of TYLCV-C1/AC1 gene in five major Asian countries. Based on publically available nucleotide sequence data the Codon usage pattern, Evolutionary and Phylogeographic reconstruction was carried out. The study revealed the presence of significant variation between the codon bias indices in all the selected regions. Implying that the codon usage pattern indices (eNC, CAI, RCDI, GRAVY, Aromo) are seriously affected by selection and mutational pressure, taking a supremacy in shaping the codon usage bias of viral gene. Further, the tMRCA age was 1853, 1939, 1855, 1944, 1828 for China, India, Iran, Oman and South Korea, respectively for TYLCV-C1/AC1 gene. The integrated analysis of Codon usage bias, Evolutionary rate and Phylogeography analysis in viruses signifies the positive role of selection and mutational pressure among the selected regions for TYLCV (C1/AC1) gene

The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses

Background and Aim: Pestivirus, a genus of the Flaviviridae family, comprises viruses that affect bovines, sheep, and pigs. Symptoms, including hemorrhagic syndromes, abortion, respiratory complications, and deadly mucosal diseases, are produced in infected animals, which cause huge economic losses to the farmers. Bovine viral diarrhea virus-1, bovine viral diarrhea virus-2, classical swine fever virus, border disease virus, Bungowannah, Hobi-like, and atypical porcine pestivirus belonging to the Pestivirus genus were selected for the study. This study aimed to estimate the codon usage bias and the rate of evolution using the glycoprotein E2 gene. Furthermore, codon usage bias analysis was performed using publicly available nucleotide sequences of the E2 gene of all seven Pestiviruses. These nucleotide sequences might elucidate the disease epidemiology and facilitate the development of designing better vaccines. Materials and Methods: Coding sequences of the E2 gene of Pestiviruses A (n = 89), B (n = 60), C (n = 75), D (n = 10), F (n = 07), H (n = 52), and K (n = 85) were included in this study. They were analyzed using different methods to estimate the codon usage bias and evolution. In addition, the maximum likelihood and Bayesian methodologies were employed to analyze a molecular dataset of seven Pestiviruses using a complete E2 gene region. Results: The combined analysis of codon usage bias and evolutionary rate analysis revealed that the Pestiviruses A, B, C, D, F, H, and K have a codon usage bias in which mutation and natural selection have played vital roles. Furthermore, while the effective number of codons values revealed a moderate bias, neutrality plots indicated the natural selection in A, B, F, and H Pestiviruses and mutational pressure in C, D, and K Pestiviruses. The correspondence analysis revealed that axis-1 significantly contributes to the synonymous codon usage pattern. In this study, the evolutionary rate of Pestiviruses B, H, and K was very high. The most recent common ancestors of all Pestivirus lineages are 1997, 1975, 1946, 1990, 2004, 1990, and 1990 for Pestiviruses A, B, C, D, F, H, and K, respectively. This study confirms that both mutational pressure and natural selection have played a significant role in codon usage bias and evolutionary studies. Conclusion: This study provides insight into the codon usage bias and evolutionary lineages of pestiviruses. It is arguably the first report of such kind. The information provided by the study can be further used to elucidate the respective host adaptation strategies of the viruses. In turn, this information helps study the epidemiology and control methods of pestiviruses

Evaluation of Frictional Contact Stresses in Spur and Helical Gears

Stress analysis of gears has become a popular area of research in order to reduce the failures and to optimize the design of gears. Friction between gears causes detrimental effects on gear surface contacts, but there is no effective method to determine the frictional effects on these contacts. Inclusion of friction in the study of gear contact is sparse. Also, friction depends on various other parameters, which are in turn ambiguous to evaluate. Hence, a quantitative study of frictional effects on gear contact problem is therefore essential. Thus, to solve the present problem, a dimensionless factor is needed to be developed which would account for the friction in gear contact stress calculations. A simplified gear contact stress evaluation technique which includes friction needs to be developed. In this work, a 3D frictional Finite Element Method (FEM) was employed for the gear frictional study. A newly developed ANSYS APDL involute profile program for spur and helical gears was used for FE modelling. Frictional coefficient and helix angle were considered as the important geometrical parameters in determining the contact stresses. A few cases of spur and helical gear system were analysed using analytical (AGMA calculations) and experimental test data for validation purposes. The experimentation was carried out using a customised experimental setup, Gear Dynamic Stress Test Rig (GDSTR). The experimental results provided a good correlation with the results of the developed 3D FE models. The validated FE models were analysed and the results showed 15% to 22% rise in gear contact stresses for increased frictional coefficients, which is significant. The FE analysis was further extended and a parametric study was carried out. This work developed a dimensionless friction factor and its function which estimates the significant rise of contact stresses in gears. The mathematically correlated KF function was verified and the inclusion of this factor provides better frictional contact stress evaluation in gears. This provides a simplified frictional measure in gear contact stress calculations

Stable degradation of catechol by <i style="">Pseudomonas</i> sp. strain NGK1 encapsulated in alginate and polyurethane foam

568-572Catechol is a terminal metabolite formed during the degradative pathways of various aromatic compounds, generally pollutants. Pseudomonas sp. strain NGK1 (NCIM 5120), a soil microbe, is capable of utilizing catechol as the carbon and energy source. This bacterium was encapsulated in alginate and polyurethane foam (PUF). The degradation rate of 20 and 40 mM of catechol in shaken batch cultures, repeated batch cultures, and continuous degradation in a packed bed reactor by free cells was compared with the degradation rate by alginate-and PUF-immobilized cells. The degradation for 72 hrs incubation in batch cultures was: free cells, 6 and 4; alginate-encapsulated cells, 15 and 18; and PUF-encapsulated cells, 18 and 30 mM catechol. Further, the alginate- and PUF-encapsulated cells were used in repeated batch degradation of catechol. Alginate- and PUF-encapsulated cells were found more efficient for the degradation than free cells. Continuous degradation in a packed bed reactor was also investigated. The efficiency of both the immobilized systems for the degradation of catechol was examined

Analysis of codon usage bias of classical swine fever virus

Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5' and 3' end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/ codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India