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

Research (Published online: 29-07-2022)

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

Mohammad Shueb, Shashanka K. Prasad, Kuralayanapalya Puttahonnappa Suresh, Uma Bharathi Indrabalan, Mallikarjun S. Beelagi, Chandan Shivamallu, Ekaterina Silina, Victor Stupin, Natalia Manturova, Shiva Prasad Kollur, Bibek Ranjan Shome, Raghu Ram Achar and Sharanagouda S. Patil

Veterinary World, 15(7): 1857-1868

ABSTRACT

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.

Keywords: codon usage bias, evolutionary analysis, Flaviviridae, glycoprotein E2, India, Pestivirus.

Difference in cytological findings of healthy and conjunctivitis/keratoconjunctivitis affected canine eyes between variably experienced evaluators

Research (Published online: 28-07-2022)

33. Difference in cytological findings of healthy and conjunctivitis/keratoconjunctivitis affected canine eyes between variably experienced evaluators

Inese Berzina, Anastasija Terentjeva and Liga Kovalcuka

Veterinary World, 15(7): 1852-1856

ABSTRACT

Background and Aim: Cytology investigations are a frequent part of ophthalmological examination. We aimed to assess whether the cytological findings of healthy and conjunctivitis/keratoconjunctivitis samples differed based on the evaluator's experience.

Materials and Methods: A study evaluated healthy eyes (n = 40) and eyes affected with keratoconjunctivitis and/ or conjunctivitis (n = 28) in dogs. An ophthalmological examination was performed before sampling the eyes using a sterile cotton swab. An evaluator with theoretical experience and one with undergone clinical pathology residency training performed cytology blinded to the clinical findings.

Results: In the healthy eyes group, the agreement between the evaluators for cellularity was nonexistent, while that for cell preservation and mucus content was fair. In the affected eyes group, the agreement for cellularity and mucus content was moderate, while that for cell preservation was fair. The inadequate sample rate differed significantly between the two evaluators in the healthy eyes group (p = 0.006) but not in the affected eyes group (p = 0.083). Bacterial presence was detected by both evaluators, and the findings did not differ statistically from the bacteriology results (p = 0.05). Significant variations were noted in the differential cell count; the mean count of the superficial epithelial cells and goblet cells of the healthy eyes group (p < 0.05) and that of the basal/intermediate cells and neutrophils of the affected eyes (p < 0.05) showed significant differences.

Conclusion: The evaluator's experience significantly affected the differential cell count in both the healthy and affected eyes groups. Neutrophil degeneration was not observed by the less experienced evaluator, whereas bacteria were detected equally well by both the evaluators.

Keywords: conjunctival cytology, microscopy experience, neutrophil morphology.

Percent positivity and phylogenetic analysis of Mycoplasma gallisepticum and Mycoplasma synoviae in commercial poultry from the different States of India

Research (Published online: 28-07-2022)

32. Percent positivity and phylogenetic analysis of Mycoplasma gallisepticum and Mycoplasma synoviae in commercial poultry from the different States of India

Pranoti Giram, Pankhudi Bhutada, Chhagan Prajapati, Santosh S. Koratkar, Sachin Patil, Devender Hooda, Vinay Rale, and Satish S. Tongaonkar

Veterinary World, 15(7): 1843-1851

ABSTRACT

Background and Aim: The Indian and global poultry industries suffer significant economic losses due to Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) infections, which adversely affect egg production, hatchability, weight gain, and feed efficiency in farms, thus decreasing the overall production efficiency. This study aimed to determine the percent positivity and phylogenetic analysis of MG, MS, and co-infection of both mycoplasmas in commercial poultry farms across different states of India from 2017 to 2021.

Materials and Methods: A total of 3620 tracheal or choacal swabs were collected from breeder and layer farms showing clinical signs of avian mycoplasma infections from commercial poultry farms across India, and the percent positivity for MG, MS, and co-infection of both mycoplasmas were determined by Polymerase chain reaction using the 16S rRNA and vlhA genes amplification, respectively. Phylogenetic analysis was carried out by sequencing the mgc2 and vlhA genes of 2 samples of MG and 24 samples of M. synoviae to gain insight into the genetic variability of Indian strains. The data were then compared with other Indian strains, vaccines strains, and strains from other countries.

Results: Our data shows the percent positivity of MG, MS, and co-infection of both MG and MS was 6.43%, 23.61%, and 15.49%, respectively. The phylogenetic relationship between MG and MS was determined using the vlhA and mgc2 genes, revealing two samples of MG and 24 samples of MS clustered with other Indian strains. M. synoviae MSM22 and previously studied M. synoviae MGS 482 clustered with vaccine strain M. synoviae MS-H.

Conclusion: Mycoplasma synoviae infections in breeder, layer, and in both is predominant compared to MG across the states investigated in India. Sequenced samples of MG and MS showed evolutionary relationships with the previously studied Indian strains of MG and MS. These findings support our view that monitoring chickens for avian mycoplasma infections are of paramount significance. It further lends credence to the contention that such information will pave the way for the development of a home-grown vaccination control program and thus safeguard the poultry sector against mycoplasma infections.

Keywords: epidemiology, India, Mycoplasma gallisepticum, Mycoplasma synoviae, phylogeny, polymerase chain reaction.

First report of canine morbillivirus infection of adipose tissue-derived stem cells from dogs with distemper

Research (Published online: 27-07-2022)

31. First report of canine morbillivirus infection of adipose tissue-derived stem cells from dogs with distemper

Fabiola Altamirano-Samaniego, Javier Enciso-Benavides, Nancy Rojas, Juan Manuel Iglesias-Pedraz, Nathaly Enciso, Matia Fossatti and Javier Enciso

Veterinary World, 15(7): 1835-1842

ABSTRACT

Background and Aim: Ribonucleic acid viruses remain latent in different cell types, including mesenchymal stem cells; however, the distemper virus remains undetected in these cells. This study aimed to determine whether adipose stem cells (ASCs) from dogs with distemper disease are infected with the canine morbillivirus (CM).

Materials and Methods: Twelve dogs with the neurological phase of the disease and who were positive for CM by reverse transcription polymerase chain reaction (RT-PCR), were studied. ASCs from adipose tissue of the lesser omentum of these infected dogs were isolated and characterized. Direct fluorescence was used to detect the viral antigen in cell cultures. Flow cytometry and RT-PCR identified detectable quantities of the virus in two cultures, while electron microscopy confirmed the CM particles within ASCs.

Results: This study revealed that ASCs of the omentum of dogs with distemper disease can be infected with CM, indicating their possible involvement in this virus latency and persistence. This suggests that its detection should be considered within the quality control process of stem cells intended for regenerative medicine.

Conclusion: To the best of our knowledge, this is the first study that demonstrates that omentum ASCs from dogs with distemper disease can be infected with CM and may be involved in viral latency or persistence. Our study also suggests that the detection of CM should be considered within the quality control process of stem cells intended for regenerative medicine.

Keywords: adipose stem cells, canine distemper disease, canine morbillivirus, cell therapy, viral latency.

Identification and molecular characterization of simian endogenous retrovirus in Macaca fascicularis and Macaca nemestrina from captive breeding facilities in Bogor, Indonesia

Research (Published online: 27-07-2022)

30. Identification and molecular characterization of simian endogenous retrovirus in Macaca fascicularis and Macaca nemestrina from captive breeding facilities in Bogor, Indonesia

Fitri Luthfianti Nur Annisaa, Uus Saepuloh, Diah Iskandriati and Joko Pamungkas

Veterinary World, 15(7): 1827-1834

ABSTRACT

Background and Aim: Endogenous retroviruses (ERVs) found in all vertebrates, including non-human primates (NHPs), are known to be genetically inherited. Thus, recent studies have explored ERVs for human immunodeficiency virus vaccine development using human ERV (HERV) due to the hypervariability of exogenous retroviruses which cause conventional vaccines to be ineffective. HERV was also found to be able to induce an immune response in cancer patients. This study aimed to identify and molecularly characterize ERVs from Indonesian NHPs: Macaca fascicularis and Macaca nemestrina. Then, we described the phylogenetic relationship of these isolates with those of the simian ERVs (SERVs) characterized in other species and countries.

Materials and Methods: First, 5 mL of whole blood samples was taken from 131 long-tailed macaques and 58 pig-tailed macaques in captive breeding facilities at Bogor, Indonesia, for DNA extraction. Next, the DNA samples were screened using the SYBR Green real-time polymerase chain reaction (PCR) technique with specific primers for env (simian retroviruses [SRV]1-5 7585U19 and SRV1-5 7695L21). Positive SERV results were those with cycle threshold (CT) values < 24 (CT < 24) and melting temperature (TM) ranges of 80°C–82°C. Then, whole-genome nucleotide sequences from two pig-tailed macaques samples detected as positive SERV were generated using a nucleic acid sequencing technique which utilized the walking primer method. Subsequently, the sequences were analyzed using bioinformatics programs, such as 4Peaks, Clustal Omega, and BLAST (NCBI). Subsequently, a phylogenetic tree was constructed using the neighbor-joining method in MEGA X.

Results: SYBR Green real-time PCR amplification results indicated that SERV (Mn B1 and Mn B140910)-positive samples had CT values of 22.37–22.54 and TM of 82°C. Moreover, whole-genome sequences resulted in 7991 nucleotide sequences, comprising long terminal repeat, gag, pro, pol, and env genes identical between the sequenced samples. Furthermore, the phylogenetic tree results indicated that both samples from M. nemestrina had 99%–100% nucleotide identities to the Mn 92227 sample identified at the National Primate Center University of Washington (NaPRC UW) which was imported from Indonesia in 1998, confirmed as a novel SERV strain. The phylogenetic tree results also indicated that although SERV whole-genome nucleotide and env amino acid sequences were clustered with SRV-2 (identity values of 82% and 79%, respectively), they had a 99%–100% nucleotide identity to Mn 92227. Meanwhile, the gag, pro, and pol amino acids were clustered with SRV-1, SRV-3, SRV-4, SRV-5, SRV-8, and SERV/1997, with 82% and 88% identity values.

Conclusion: Based on the SYBR Green real-time PCR profiles generated, similarities with Mn 92227 were observed. Subsequent phylogenetic analysis confirmed that both samples (Mn B1 and Mn B140919) from pig-tailed macaques in the country of origin were novel SERV strains at NaPRC UW. Therefore, it could be used in biomedical research on ERVs.

Keywords: Macaca fascicularis, Macaca nemestrina, retrovirus, simian endogenous retroviruses.

The effect of spices Coriandrum sativum L., Trigonella foenum-graecum L., Pimpinella anisum L., and their combinations on growth performance, carcass trait, and hematobiochemical parameters in broiler chicken

Research (Published online: 26-07-2022)

29. The effect of spices Coriandrum sativum L., Trigonella foenum-graecum L., Pimpinella anisum L., and their combinations on growth performance, carcass trait, and hematobiochemical parameters in broiler chicken

Samira Meradi, Ahmed Messaï and Miloud Aouachria

Veterinary World, 15(7): 1821-1826

ABSTRACT

Background and Aim: The incorporation of herbs and species has been shown to enrich the food with antioxidants and bioactive antimicrobial compounds, thereby preserving the safety and productivity of broiler chicken production. This study aimed to determine the effects of three phytogenic feed additives (PHT) on certain zootechnical and hematobiochemical parameters in broiler chickens. Coriandrum sativum L. (coriander), Pimpinella anisum L. (green anise), and Trigonella foenum-graecum L. (fenugreek) were used to formulate the PHT.

Materials and Methods: A total of 360 1-day-old Cobb broilers for 42 days were randomly assigned to four dietary treatment groups: A control group (CTLG) and three groups fed a basal diet supplemented with 3% of coriander (PHT1G), 3% of a combination 50% coriander-50% fenugreek (PHT2G), and finally, 3% of a combination 50% coriander-50% green anise (PHT3G), respectively, and each experimental group included three repetitions of 30 birds. Zootechnical parameters, carcass productivity, and hematobiochemical properties were measured.

Results: The birds in the PHT3G had the greatest body weight and organ weight (p < 0.05). However, the weight of abdominal fat remained unchanged. The same group of broilers had a significantly (p < 0.05) higher lymphocyte level of 120.103/μL, followed by the PHT2G, which had 80.103/μL. The levels of monocytes in the PHT2G and PHT3G were 66.103/μL and 60.103/μL, respectively. Regarding granulocytes, we observed 200.103/μL in the PHT2 group and 102.103/μL in the PHT3G. There was a statistically significant difference (p < 0.05) between the uric acid levels of the PHT1G, PHT2G, and PHT3G, with 50.4 mg/L, 59.84 mg/L, and 47.29 mg/L, respectively. All experimental groups had significantly lower uric acid concentrations than the control group (84.36 mg/L).

Conclusion: The use of phytogenic feed additives may positively affect both weight gain and hematobiochemical parameters in broiler chicken, particularly the levels of various white blood cell subtypes and the uric acid rate.

Keywords: broilers, blood parameters, natural feed additive, performances, spices seed.

Estimation of the probability risks of African swine fever outbreaks using the maximum entropy method in North Sumatra Province, Indonesia

Research (Published online: 26-07-2022)

28. Estimation of the probability risks of African swine fever outbreaks using the maximum entropy method in North Sumatra Province, Indonesia

Roza Azizah Primatika, Etih Sudarnika, Bambang Sumiarto and Chaerul Basri

Veterinary World, 15(7): 1814-1820

ABSTRACT

Background and Aim: African swine fever (ASF) is an infectious disease and a major viral pig disease that threatens pork production in several locations globally. The mortality rate of ASF in domestic pigs is very high, causing a decrease in pig populations and significant economic losses for farmers. Environmental or ecological risk factors are the most important associated with the spread of the ASF virus. Environmental (or ecological) niche models are commonly used to estimate the probability of an event using the maximum entropy (Maxent) method. This study aimed to estimate the probability risk of future ASF outbreaks in North Sumatra, Indonesia.

Materials and Methods: Secondary data from the National Animal Health System Database (iSIKHNAS), including data on the ASF outbreaks of 2019–2020 in North Sumatra, Indonesia, were used in this study. The first analysis performed involved the identification of environmental risk factors using multiple regression analysis. The second analysis performed was the estimation of probability risk for future ASF outbreaks in North Sumatra, Indonesia, using the Maxent method. Data processing was performed using Microsoft Excel, ArcGIS version 10.5 software (ESRI, California, United States), Maxent version 3.4.4 software, and Rstudio (http://www.r-project.org/).

Results: The Maxent method was found to be highly accurate with a statistically significant area under the curve value of 0.860. The greatest contributing environmental factor identified by the model was the harbor, which contributed 57%. The range of high probability risk of future ASF outbreaks was found to be 0.723–0.84.

Conclusion: The estimation of the highest probability risk of future ASF outbreaks in North Sumatra, Indonesia, was 0.723–0.84. The most contributing environmental factor identified using the Maxent method was harbors, at 57%. This methodology can be used to carry out subsequent ASF analyses and contribute to developing prevention and control strategies in this area.

Keywords: African swine fever, environmental niche models, maximum entropy, probability risk.