scholarly journals Molecular characterization and phylogenetic analysis of bovine ephemeral fever viruses in Khuzestan province of Iran in 2018 and 2020

2022 ◽  
Vol 18 (1) ◽  
Author(s):  
Seyedeh Elham Rezatofighi ◽  
Khalil Mirzadeh ◽  
Fahimeh Mahmoodi
Keyword(s):  
Phylogenetic Analysis ◽  
Middle East ◽  
Molecular Characterization ◽  
Rna Virus ◽  
Geographical Area ◽  
Viral Disease ◽  
Multiple Sequence ◽  
Khuzestan Province ◽  
Bovine Ephemeral Fever ◽  
Southwest Of Iran

Abstract Background Bovine ephemeral fever (BEF) is an arthropod-borne viral disease caused by the BEF virus (BEFV). This single-stranded RNA virus that affects cattle and water buffalo is endemic in tropical and subtropical regions including Iran. While BEF is a major disease of cattle in Iran, information regarding its agent, molecular characterization, and circulating viruses are highly limited. The current study aimed to, firstly, determine the genetic and antigenic characteristics of BEFV strains in Khuzestan province in Southwest of Iran in 2018 and 2020 and, secondly, to compare them with strains obtained from other areas. Results By phylogenetic analysis based on the Glycoprotein gene, BEFV strains were divided into four clusters of Middle East, East Asia, South Africa, and Australia; in which the 2018 and 2020 Iranian BEFV strains were grouped in the Middle East cluster with the Turkish, Indian, and Israeli strains. Depending on the chronology and geographical area, the outbreaks of Turkey (2020), Iran (2018 and 2020), and India (2018 and 2019) are proposed to be related. These BEFVs had the highest identity matrix and the lowest evolutionary distance among the studied strains. Multiple sequence alignment of G1, G2, and G3 antigenic sites showed that these neutralizing epitopes are highly conserved among the strains of the Middle East cluster; however, the strains previously identified in Iran differed in three amino acids placed in G1 and G2 epitopes. Conclusion The findings revealed that BEFVs circulating in the Middle East are closely related phylogenetically and geographically. They also have similar antigenic structures; therefore, developing a vaccine based on these strains can be effective for controlling BEF in the Middle East.

scholarly journals Molecular Characterization and Phylogenetic Analysis of Bovine Ephemeral Fever Viruses in Khuzestan Province of Iran From 2018 to 2020

2021 ◽  
Author(s):  
Seyedeh Elham Rezatofighi ◽  
Khalil Mirzadeh ◽  
Fahimeh Mahmoodi
Keyword(s):  
Phylogenetic Analysis ◽  
Middle East ◽  
Molecular Characterization ◽  
Rna Virus ◽  
Geographical Area ◽  
Viral Disease ◽  
Multiple Sequence ◽  
Khuzestan Province ◽  
Bovine Ephemeral Fever ◽  
Southwest Of Iran

Abstract Background Bovine ephemeral fever (BEF) is an arthropod-borne viral disease caused by the BEF virus (BEFV). This single-stranded RNA virus that affects cattle and water buffalo is endemic in tropical and subtropical regions including Iran. While BEF is a major disease of cattle in Iran, information regarding its agent, molecular characterization, and circulating viruses are highly limited. The current study aimed to, firstly, determine the genetic and antigenic characteristics of BEFV strains in Khuzestan province in Southwest of Iran from 2018 to 2020 and, secondly, to compare them with strains obtained from other areas. Results By phylogenetic analysis based on the Glycoprotein gene, BEFV strains were divided into four clusters of Middle East, East Asia, South Africa, and Australia; in which the 2018 and 2020 Iranian BEFV strains were grouped in the Middle East cluster with the Turkish, Indian, and Israeli strains. Depending on the chronology and geographical area, the outbreaks of Turkey (2020), Iran (2018 and 2020), and India (2018 and 2019) are proposed to be related. These BEFVs had the highest identity matrix and the lowest evolutionary distance among the studied strains. Multiple sequence alignment of G1, G2, and G3 antigenic sites showed that these neutralizing epitopes are highly conserved among the strains of the Middle East cluster; however, the strains previously identified in Iran differed in three amino acids placed in G1 and G2 epitopes. Conclusion The findings revealed that BEFVs circulating in the Middle East are closely related phylogenetically and geographically. They also have similar antigenic structures; therefore, developing a vaccine based on these strains can be effective for controlling BEF in the Middle East.

scholarly journals Molecular characterization of porcine epidemic diarrhoea virus (PEDV) in Poland reveals the presence of swine enteric coronavirus (SeCoV) sequence in S gene

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258318
Author(s):  
Marta Antas ◽  
Monika Olech ◽  
Anna Szczotka-Bochniarz
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rna Virus ◽  
Economic Losses ◽  
High Morbidity ◽  
Antigenic Analysis ◽  
S Gene ◽  
Porcine Epidemic Diarrhoea Virus ◽  
Diarrhoea Virus

Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5’ end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.

scholarly journals Molecular Characterization of Leishmania RNA virus 2 in Leishmania major from Uzbekistan

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 830 ◽  
Author(s):  
Yuliya Kleschenko ◽  
Danyil Grybchuk ◽  
Nadezhda S. Matveeva ◽  
Diego H. Macedo ◽  
Evgeny N. Ponirovsky ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cutaneous Leishmaniasis ◽  
Molecular Characterization ◽  
Leishmania Major ◽  
Geographical Origin ◽  
Rna Virus ◽  
Viral Sequences

Here we report sequence and phylogenetic analysis of two new isolates of Leishmania RNA virus 2 (LRV2) found in Leishmania major isolated from human patients with cutaneous leishmaniasis in south Uzbekistan. These new virus-infected flagellates were isolated in the same region of Uzbekistan and the viral sequences differed by only nineteen SNPs, all except one being silent mutations. Therefore, we concluded that they belong to a single LRV2 species. New viruses are closely related to the LRV2-Lmj-ASKH documented in Turkmenistan in 1995, which is congruent with their shared host (L. major) and common geographical origin.

scholarly journals Isolation, molecular and phylogenetic analysis of porcine encephalomyocarditis virus strain HLJ in China

2020 ◽  
Author(s):  
Xueting Yin ◽  
Peng Liu ◽  
Haixin Liu ◽  
Yue Zhang ◽  
Ghulam Abbas ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Virus ◽  
Acute Myocarditis ◽  
Electron Microscopic Observation ◽  
Immunofluorescence Assay ◽  
Encephalomyocarditis Virus ◽  
Swine Industry ◽  
Electron Microscopic ◽  
Multiple Sequence ◽  
Wide Range

Abstract Background Encephalomyocarditis virus (EMCV) is a positive single-stranded small RNA virus without envelope, which can infect a variety of mammals. Swine are the most susceptible animals, which can cause acute myocarditis and respiratory failure in piglets and reproductive failure in pregnant sows. Diseases caused by EMCV have a wide range of effects on the global swine industry. Methods The tissue grinding fluid of aborted fetus was inoculated on baby hamster kidney 21 (BHK-21) cells to obtain HLJ isolate by cell passage. The virus was identified by reverse transcriptase polymerase chain reaction (RT-PCR), electron microscopic observation and indirect immunofluorescence assay (IFA). HLJ strain was inoculated into mice for animal regression experiment. The whole genome of HLJ strain was amplified and sequenced. The molecular and phylogenetic analysis of its sequence was generated. Results HLJ strain caused the specific cytopathic effect (CPE) on BHK-21 cells and severe pathological changes in mice. Complete genome sequencing and multiple sequence alignment showed that the homology between HLJ strain and other isolates worldwide was 71.5–99.7%. Phylogenetic analysis showed that EMCV isolates fell into five clusters: lineage I, II, III, IV, and V based on the nucleotide sequences of the entire open reading frame (ORF) and VP1 gene. HLJ isolate was grouped into lineage I. Conclusions In this study, a strain of EMCV was isolated from an aborted fetus in Northeast China. The isolation of HLJ strain enriches the epidemiological database of EMCV.

scholarly journals Molecular characterization of lumpy skin disease virus (LSDV) emerged in Bangladesh reveals unique genetic features compared to contemporary field strains

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Shukes Chandra Badhy ◽  
Mohammad Golam Azam Chowdhury ◽  
Tirumala Bharani Kumar Settypalli ◽  
Giovanni Cattoli ◽  
Charles Euloge Lamien ◽  
...  
Keyword(s):  
Middle East ◽  
Molecular Characterization ◽  
Disease Virus ◽  
Skin Disease ◽  
Clinical Signs ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Lumpy Skin Disease ◽  
Lumpy Skin Disease Virus

Abstract Background Lumpy skin disease (LSD) is a contagious viral disease of cattle caused by lumpy skin disease virus (LSDV). LSD has recently spread in Asia following outbreaks in the Middle East and Europe. The disease emerged in Bangladesh in July 2019 in the Chattogram district, then rapidly spread throughout the entire country. We investigated six LSD outbreaks in Bangladesh to record the clinical signs and collect samples for diagnostic confirmation. Furthermore, we performed the molecular characterization of Bangladesh isolates, analyzing the full RPO30 and GPCR genes and the partial EEV glycoprotein gene. Results Clinical observations revealed common LSD clinical signs in the affected cattle. PCR and real-time PCR, showed the presence of the LSDV genome in samples from all six districts. Phylogenetic analysis and detailed inspection of multiple sequence alignments revealed that Bangladesh isolates differ from common LSDV field isolates encountered in Africa, the Middle East, and Europe, as well as newly emerged LSDV variants in Russia and China. Instead, they were closely related to LSDV KSGP-0240, LSDV NI2490, and LSDV Kenya. Conclusions These results show the importance of continuous monitoring and characterization of circulating strains and the need to continually refine the strategies for differentiating vaccine strains from field viruses.

scholarly journals Variant analysis of SARS-CoV-2 genomes in the Middle East

2020 ◽  
Author(s):  
Khalid Mubarak Bindayna ◽  
Shane Crinion
Keyword(s):  
Phylogenetic Analysis ◽  
Middle East ◽  
Variant Calling ◽  
Gene Variants ◽  
Multiple Sequence ◽  
Upstream Gene ◽  
Depth Analysis ◽  
Show Evidence ◽  
Variant Analysis ◽  
Genome Variants

AbstractBackgroundCoronavirus (COVID-19) was introduced into society in late 2019 and has now reached over 26 million cases and 850,000 deaths. The Middle East has a death toll of ∼50,000 and over 20,000 of these are in Iran, which has over 350,000 confirmed cases. We expect that Iranian cases caused outbreaks in the neighbouring countries and that variant mapping and phylogenetic analysis can be used to prove this. We also aim to analyse the variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to characterise the common genome variants and provide useful data in the global effort to prevent further spread of COVID-19.MethodsThe approach uses bioinformatics approaches including multiple sequence alignment, variant calling and annotation and phylogenetic analysis to identify the genomic variants found in the region. The approach uses 122 samples from the 13 countries of the Middle East sourced from the Global Initiative on Sharing All Influenza Data (GISAID).FindingsWe identified 2200 distinct genome variants including 129 downstream gene variants, 298 frame shift variants, 789 missense variants, 1 start lost, 13 start gained, 1 stop lost, 249 synonymous variants and 720 upstream gene variants. The most common, high impact variants were 10818delTinsG, 2772delCinsC, 14159delCinsC and 2789delAinsA. Variant alignment and phylogenetic tree generation indicates that samples from Iran likely introduced COVID-19 to the rest of the Middle East.InterpretationThe phylogenetic and variant analysis provides unique insight into mutation types in genomes. Initial introduction of COVID-19 was most likely due to Iranian transmission. Some countries show evidence of novel mutations and unique strains. Increased time in small populations is likely to contribute to more unique genomes. This study provides more in depth analysis of the variants affecting in the region than any other study.FundingNone

Morphological, histological and molecular characterization of Myxidium cf. rhodei infecting the kidney of Rutilus rutilus

2020 ◽  
Vol 141 ◽  
pp. 39-46
Author(s):  
MD Dorjievna Batueva ◽  
X Pan ◽  
J Zhang ◽  
X Liu ◽  
W Wei ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Rutilus Rutilus ◽  
Longitudinal Axis ◽  
Suture Line ◽  
Present Species ◽  
Supplementary Data

In the present study, we provide supplementary data for Myxidium cf. rhodei Léger, 1905 based on morphological, histological and molecular characterization. M. cf. rhodei was observed in the kidneys of 918 out of 942 (97%) roach Rutilus rutilus (Linnaeus, 1758). Myxospores of M. cf. rhodei were fusiform with pointed ends, measuring 12.7 ± 0.1 SD (11.8-13.4) µm in length and 4.6 ± 0.1 (3.8-5.4) µm in width. Two similar pear-shaped polar capsules were positioned at either ends of the longitudinal axis of the myxospore: each of these capsules measured 4.0 ± 0.1 (3.1-4.7) µm in length and 2.8 ± 0.1 (2.0-4.0) µm in width. Polar filaments were coiled into 4 to 5 turns. Approximately 18-20 longitudinal straight ridges were observed on the myxospore surface. The suture line was straight and distinctive, running near the middle of the valves. Histologically, the plasmodia of the present species were found in the Bowman’s capsules, and rarely in the interstitium of the host. Phylogenetic analysis revealed that M. cf. rhodei was sister to M. anatidum in the Myxidium clade including most Myxidium species from freshwater hosts.

Plasma therapy a possible hope to fight against COVID-19

2020 ◽  
Author(s):  
Ravikant Piyush ◽  
Aroni Chatterjee ◽  
Shashikant Ray
Keyword(s):  
Middle East ◽  
Severe Acute Respiratory Syndrome ◽  
Viral Disease ◽  
Plasma Therapy ◽  
Therapeutic Drugs ◽  
Wild Fire ◽  
The World ◽  
Short Span ◽  
Game Changer

The world is currently going through a disastrous event and a catastrophic upheaval caused by the coronavirus disease 2019 (COVID-19). The pandemic has resulted in loss of more than 150000 deaths across the globe. Originating from China and spreading across all continents within a short span of time, it has become a matter of international emergency. Different agencies are adopting diverse approaches to stop and spread of this viral disease but still now nothing confirmatory has come up. Due to lack of vaccines and proper therapeutic drugs, the disease is still spreading like wild fire without control. An Old but very promising method- the convalescent plasma therapy could be the key therapy to stop this pandemic. This method has already proven its mettle on several occasions previously and has been found to be effective in curing the pandemics induced by Ebola, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the same group of β-Coronavirus that has resulted in the above diseases. Therefore, the role of plasma therapy is being explored for treatment of this disease. In this review, we have mainly focused on the role of convalescent plasma therapy and why its use should be promoted in fight against COVID-19, as it could turn out to be a game changer.

LegumeDB: Development of Legume Medicinal Plant Database and Comparative Molecular Evolutionary Analysis of matK Proteins of Legumes and Mangroves

2019 ◽  
Vol 15 (4) ◽  
pp. 353-362
Author(s):  
Sambhaji B. Thakar ◽  
Maruti J. Dhanavade ◽  
Kailas D. Sonawane
Keyword(s):  
Phylogenetic Analysis ◽  
Medicinal Plants ◽  
Homology Modeling ◽  
Sequence Alignment ◽  
Vigna Unguiculata ◽  
Multiple Sequence Alignment ◽  
Legume Species ◽  
Mangrove Species ◽  
Multiple Sequence ◽  
Thespesia Populnea

Background: Legume plants are known for their rich medicinal and nutritional values. Large amount of medicinal information of various legume plants have been dispersed in the form of text. Objective: It is essential to design and construct a legume medicinal plants database, which integrate respective classes of legumes and include knowledge regarding medicinal applications along with their protein/enzyme sequences. Methods: The design and development of Legume Medicinal Plants Database (LegumeDB) has been done by using Microsoft Structure Query Language Server 2017. DBMS was used as back end and ASP.Net was used to lay out front end operations. VB.Net was used as arranged program for coding. Multiple sequence alignment, phylogenetic analysis and homology modeling techniques were also used. Results: This database includes information of 50 Legume medicinal species, which might be helpful to explore the information for researchers. Further, maturase K (matK) protein sequences of legumes and mangroves were retrieved from NCBI for multiple sequence alignment and phylogenetic analysis to understand evolutionary lineage between legumes and mangroves. Homology modeling technique was used to determine three-dimensional structure of matK from Legume species i.e. Vigna unguiculata using matK of mangrove species, Thespesia populnea as a template. The matK sequence analysis results indicate the conserved residues among legume and mangrove species. Conclusion: Phylogenetic analysis revealed closeness between legume species Vigna unguiculata and mangrove species Thespesia populnea to each other, indicating their similarity and origin from common ancestor. Thus, these studies might be helpful to understand evolutionary relationship between legumes and mangroves. : LegumeDB availability: http://legumedatabase.co.in

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