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Recombination Analysis of S-Segment Genome of Crimean-Congo Hemorrhagic Fever Virus in Turkey

Journal of Research in Medical and Dental Science
eISSN No. 2347-2367 pISSN No. 2347-2545

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Research - (2020) Volume 8, Issue 4

Recombination Analysis of S-Segment Genome of Crimean-Congo Hemorrhagic Fever Virus in Turkey

Murtaza Oklu1, Ibrahim Suslu2, Cengiz Z Altuntas3 and Senol Dane4*

*Correspondence: Senol Dane, Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Nile University of Nigeria, Abuja, Nigeria, Email:

Author info »

Abstract

Background: Crimean-Congo Hemorrhagic Fever (CCHF) is an illness that caused by a tick-borne virus, which belongs to family Bunyaviridae, genus Nairovirus. It is carried on migratory birds. CCHF disease has been appeared in Europe, Asia, and Africa. Then, the disease spread in other cities in Turkey such as Yozgat, Eskisehir, Kelkit, and Corum. RNA recombination is mixing of genetic material strains from different countries into new combinations that cause RNA virus diversity. The aim of this study is the recombination analysis of complete S-segment genome among CCHFV strains in Turkey and strains from different countries.

Materials and Methods: S-segment has the strongest geographical subdivision, and the investigation S-segment genome of CCHFV explained that there are differences in nucleotide sequences between strains. Turkey is a center for distribution of migratory birds. In this study, we compared strains whit complete sequence from Russia, Bulgaria, Kosovo, Greece, Iran, Nigeria, Mauritania, Sudan, South Africa, and Mali, where have migratory birds’ flyways. The GenBank information is downloaded from www.ncbi.nlm.nih. gov in FASTA format and investigated with phylogenetic tree. Evidence of recombination is analyzed by using SimPlot and MEGA X software.

Results: The strains in Corum, Kelkit, Eskisehir, Yozgat are mainly recombinant of the strains in Iran, Russia, Bulgaria, and Nigeria in orderly.

Conclusion: This research revealed that African-Eurasian migratory bird flyways provide the way for intercontinental migration of the CCHFV that causes recombination of CCHFV in Turkey. Thus, the vaccine design should be updated as concerned of recombination of CCHFV. 

Keywords

Recombination, Crimean Congo Hemorrhagic Fever, Turkey, S-segment, Phylogenetic

Introduction

CCHF is an illness that caused by a tick-borne virus, which belongs to family Bunyaviridae, genus Nairovirus. The virus is carried on migratory birds [1,2]. CCHF disease has been appeared in Europe, Asia, and Africa and distributed from Africa, Asia, and Europe to wide range [3]. In 2002, CCHF virus cases were reported at the first time in Tokat, Turkey [4]. Then, the disease was detected from other cities such as Corum, Aydin, Yozgat, Kayseri, Eskisehir, Kayseri, and Gumushane. Only humans and sucking mice has affected from the disease and there are no clinical symptoms in other vertebrates [5]. The disease is transferred to human body with bites from infected ticks. CCHF is an important health issue around the world.

The infected ticks are carried on migratory birds and spread to enormous area on their migration flyways. The spreading of CCHF virus is caused genetic varieties which can be explained by recombination, reassortment, and mutation [3,6]. RNA viruses have ability to change their population size and high rates of mutation quickly [7]. Many data are collected from different cities and investigated to learn recombination between strains in Turkey, and the results showed that there is genetic diversity between infected ticks. Also, in our study we compared the genomes of CCHF viruses from different countries, which are chosen about of recombination relation with Turkey, such as Russia, Bulgaria, Kosovo, Greece, Iran, Nigeria, Mauritania, Sudan, South Africa, and Mali. The reason of analyzing CCHF virus from different countries is to understand better how infected virus spread in an enormous area. The aim of this study is the recombination analysis of complete S-segment genome among CCHFV strains in Turkey and strains from different countries.

Materials and Methods

Recombination has a significant impact for designing genetic differences in RNA viruses [8]. CCHF virus contains three segments, which are S, M, and L, genome and depend on phylogenetic analysis, S-segment has the strongest geographical subdivision [9]. The result of investigated the S-segment genome of CCHFV explained that there are differences in nucleotide sequences between cities. The GenBank information is downloaded from www.ncbi.nlm. nih.gov in FASTA format and investigated with phylogenetic tree. Evidence of recombination is analyzed by using SimPlot and MEGA X software. SimPlot program performed boot scan method for analyzing the recombination of the strains and shows the consequences with a graphical figure. MEGA X software program is used the determine the situation of the strains in a phylogenetic tree. First, the strains are chosen from the cities of Turkey, then the nucleotide-blast method is used to determine which strains have similarities with the chosen strains. Then, the data of the strains are collected in a file for using in SimPlot and MEGA X software. The data is used in MEGA X software to find out phylogenetic tree of the chosen strains. After that, the data is transferred to SimPlot program to explore which strains have recombination with each other. The strains are marked with different colors to determine and understand the graphic.

Results

The strains are supplied from www.ncbi.nlm. nih.gov for detecting the recombination between each other. Crimean-Congo hemorrhagic fever virus is spread around the world from different countries with immigrant birds. A strain has been found from a patient in Turkey was genetically quite different than the previous strains which found in Tukey, but the strain is related with a virus which found in Greece [10]. For this project, some strains are collected from various countries such as Turkey, Russia, Bulgaria, Nigeria, Mauritania, Sudan, Iran, Greece, and Kosovo. Name of the viruses, countries, year of isolations, and GenBank accession numbers are given in Table 1 to show the data of the strain in Table 1. The strains in Corum, Kelkit, Eskisehir, Yozgat, which Turkish cities, are mainly recombinant of the strains in Iran, Russia, Bulgaria, and Nigeria in orderly.

Name of virus isolate Country Year of isolation GenBank accession no S-segment
Turkey-Kelkit 06 Turkey 2006 GQ337053
Yozgat 19-2012 Turkey 2012 KR092375
Eskisehir 23-2012 Turkey 2012 KR092376
Corum 1094-2011 Turkey 2011 KR092378
9553/2001 Kosovo 2001 AF428144
Kosovo Hoti Kosovo 1980 DQ133507
V42/81 Bulgaria 1981 GU477489
ROS/TI28044 Bulgaria 2003 AY277672
66/08-Rodopi Greece 2008 EU871766
46-ST-2012 Russia 2012 KR814841
Kashmanov Russia 1967 DQ211644
ROS/HUVLV-100 Russia 2002 DQ206447
Ast133 Russia 2012 KX056061
Iran-Isfahan78 Iran 2013 KJ027522
Iran-Gilan69 Iran 2012 KJ027521
Iran-Kerman43 Iran 2013 KJ196326
Iran-Tehran65 Iran 2011 KJ566219
Iran-Zahedan19 Iran 2012 KJ676542
UCCR4401 Nigeria 1996 KY484036
ArD39554 Mauritania 1984 DQ211641
Sudan_Al_Fulah_3-2008 Sudan 2008 GQ862371

Table 1: Crimean-Congo Hemorrhagic Fever virus isolates used in this study, with related countries of origin, collection date, and S-segment GenBank accession numbers.

The result of Figure 1A, from SimPlot shows that the strains from Yozgat, Nigeria, Bulgaria, and Russia have recombination between each other. Yozgat strain is used as query for finding out recombination possibilities with the others. TURKEY-YOZGAT19-2012-KR092375 has recombination with, NIGERIA-UCCR4401- KY484036 in position of 450-630 and 1,150- 1,370, BULGARIA-V42/81-GU477489 in position of 150-200, 250-430, 730-850, and 930-1,150, and RUSSIA-AST133-KX056061 in position of 1,370-1,570.

medical-dental-science-recombination

Figure 1A. TURKEY-YOZGAT19-2012-KR092375 is the query of the figure and showed a recombination with NIGERIA-UCCR4401-KY484036, BULGARIA-V42/81-GU477489, and RUSSIA-AST133-KX056061.

The result of Figure 1B from SimPlot shows that the strains from Corum, Mauritania, Bulgaria, and Russia have recombination between each other. Corum strain is used as query for finding out recombination possibilities with the others. TURKEY-CORUM1094_2011-KR092378 has recombination with, MAURITANIA-ARD39554- DQ211641 in position of 420-680 and 1,100- 1,450, BULGARIA-AY277676 in position of 100- 220 and 700-900, RUSSIA-ROS/HUVLV-100- DQ206447 in position of 220-420, 900-1,100, and 1,450-1,580.

medical-dental-science-recombination

Figure 1B. TURKEY-CORUM1094_2011-KR092378 is the query of the figure and showed a recombination with MAURITANIA-ARD39554-DQ211641, BULGARIA-AY277676, and RUSSIA-ROS/HUVLV_100-DQ206447.

The result of Figure 1C from SimPlot shows that the strains from Eskisehir, Russia, Iran, and Greece have recombination between each other. Eskisehir strain is used as query for finding out recombination possibilities with the others. TURKEY-ESKISEHIR23-2012-KR092376 has recombination with RUSSIA-AST133-KX056061 in position of 200-420, 470-500, 550-820, and 1,450-1,550, IRAN-ZAHEDAN19-KJ676542 in position of 820-1,100, and GREECE-66/08RODOPIEU871766 in position of 1,100-1,450.

medical-dental-science-recombination

Figure 1C. TURKEY-ESKISEHIR23-2012-KR092376 is the query of the figure and showed a recombination with RUSSIA-AST133-KX056061, IRAN-ZAHEDAN19-KJ676542, and GREECE-66/08RODOPI-EU871766.

The result of Figure 1D from SimPlot shows that the strains from Kelkit, Russia, Sudan, and Kosovo have recombination between each other. Kelkit strain is used as query for finding out recombination possibilities with the others. TURKEY-KELKIT06-GQ337053 has recombination with KOSOVO-9553/2001- AF428144 in position of 200-250 and 780-1,180, SUDAN-SUDAN_AL-FULAH_3-2008-GQ862371 in position of 440-560, 1,180-1,250, and 1,320- 1,520, and RUSSIA-KASHMANOV-DQ211644 in position of 100-200, 250-450, 570-770, 950- 1,050, and 1,500-1600.

medical-dental-science-recombination

Figure 1D. TURKEY-KELKIT06-GQ337053 is the query of the figure and showed a recombination with KOSOVO-9553/2001-AF428144, SUDANSUDAN_ AL-FULAH_3-2008-GQ862371, and RUSSIA-KASHMANOV-DQ211644.

In Figure 1e, phylogenetic tree shows that how the strains from various countries close each other by using MEGA X Software. Strains from the same countries have more similarities than others because of that they have close relation with each other.

medical-dental-science-recombination

Figure 1E. The strains from different countries compared in a phylogenetic tree by using MEGA X software.

Discussion

Nowadays, a big increase is seen in the incidence of CCHF disease in Turkey. The results of the present study support that the tick viruses are migrated from northwestern Africa to Europe by migratory birds [11]. The migratory birds’ flyways have a significant effect to spreading of CCHF virus. The analyzes of strains from different cities in Turkey have similarities on strains from other countries because of recombination from infected viruses that carried on migration bird flyways.

This research revealed that African-Eurasian migratory bird flyways provide the way for intercontinental migration of the CCHFV that might cause recombination of CCHFV in Turkey. Considering the recombination and reassortment in CCHF virus indicates that common isolates in the area has been altered in genetical and serological way from the viruses [5]. Thus, the vaccine design should be updated as concerned of recombination of CCHFV.

Conclusion

Analysis of complete S-segment genome among CCHFV strains in Turkey and strains from different countries revealed that all strains in Turkey have recombination.

References

Author Info

Murtaza Oklu1, Ibrahim Suslu2, Cengiz Z Altuntas3 and Senol Dane4*

1Department of Computer Science, University of Houston-Downtown, Houston, TX 77002, USA
2Department of Computer Science, North American University, Houston, TX 77477, USA
3Texas Institute of Biotechnology Education and Research (TIBER), North American University, Houston, TX 77477, USA
4Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Nile University of Nigeria, Abuja, Nigeria
 

Citation: Murtaza Oklu, Ibrahim Suslu, Cengiz Z Altuntas, Senol Dane, Recombination Analysis of S-Segment Genome of Crimean-Congo Hemorrhagic Fever Virus in Turkey, J Res Med Dent Sci, 2020, 8 (4):141-145x.

Received: 26-Jun-2020 Accepted: 20-Jul-2020

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