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Phylogeography of Crimean Congo Hemorrhagic Fever Virus

View Article: PubMed Central - PubMed

ABSTRACT

Crimean Congo hemorrhagic fever virus (CCHFV) is one of the most severe viral zoonozes. It is prevalent throughout Africa, Asia and southern Europe. Limited availability of sequence data has hindered phylogeographic studies. The complete genomic sequence of all three segments of 14 Crimean Congo hemorrhagic fever virus strains isolated from 1958–2000 in Russia, Central Asia and Africa was identified. Each genomic segment was independently subjected to continuous Bayesian phylogeographic analysis. The origin of each genomic segment was traced to Africa about 1,000–5,000 years ago. The virus was first introduced to South and Central Asia in the Middle Ages, and then spread to China, India and Russia. Reverse transfers of genomic segments from Asia to Africa were also observed. The European CCHFV genotype V was introduced to Europe via the Astrakhan region in South Russia 280–400 years ago and subsequently gradually spread westward in Russia, to Turkey and the Balkans less than 150 years ago. Only a few recombination events could be suggested in S and L genomic segments, while segment reassortment was very common. The median height of a non-reassortant phylogenetic tree node was 68–156 years. There were reassortment events within the European CCHFV lineage, but not with viruses from other locations. Therefore, CCHFV in Europe is a recently emerged zoonosis that represents a spillover from the global gene pool.

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Bootscan analysis of exemplary CCHFV genomes.The Y axis shows the percentage of phylogenetic trees with a reliably supported grouping of a query sequence with sequences indicated in the legend in a sliding window that corresponds to the x axis. A. S segment, window 400 bp, step 20 bp. B. S segment, window 500 bp, step 20 bp. C. L segment, window 400 bp, step 50 bp.
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pone.0166744.g004: Bootscan analysis of exemplary CCHFV genomes.The Y axis shows the percentage of phylogenetic trees with a reliably supported grouping of a query sequence with sequences indicated in the legend in a sliding window that corresponds to the x axis. A. S segment, window 400 bp, step 20 bp. B. S segment, window 500 bp, step 20 bp. C. L segment, window 400 bp, step 50 bp.

Mentions: Recombination within CCHFV genome segments was reported previously [17] and confirmed in subsequent studies [3]. CCHFV sequences were analyzed for recombination using the RDP 4.0 package, which utilizes a panel of algorithms. The detected cases were then visualized using bootscan graphs. Consistent with previous reports, several cases of significantly supported recombination events were found within the S segment (Fig 4A and 4B). In the L segment, only GtII (M-I) viruses isolated in DRC and Uganda displayed evidence of recombination. Interestingly, the pattern was highly mosaic and implied multiple exchanges within that group (Fig 4C). These recombination events were identified in the middle of individual chromatograms of the Nakiwogo strain sequenced in this work, ruling out experimental error (amplification of fragments of different genomes from a mixture of viruses). No reliably supported recombination events could be detected in the M segment; however, a few sequences had evidence of introduction of very short highly divergent sequences of unknown origin, suggestive of sequencing errors. In general, in CCHFV there were significantly fewer suggested recombination events than reassortment cases.


Phylogeography of Crimean Congo Hemorrhagic Fever Virus
Bootscan analysis of exemplary CCHFV genomes.The Y axis shows the percentage of phylogenetic trees with a reliably supported grouping of a query sequence with sequences indicated in the legend in a sliding window that corresponds to the x axis. A. S segment, window 400 bp, step 20 bp. B. S segment, window 500 bp, step 20 bp. C. L segment, window 400 bp, step 50 bp.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5120814&req=5

pone.0166744.g004: Bootscan analysis of exemplary CCHFV genomes.The Y axis shows the percentage of phylogenetic trees with a reliably supported grouping of a query sequence with sequences indicated in the legend in a sliding window that corresponds to the x axis. A. S segment, window 400 bp, step 20 bp. B. S segment, window 500 bp, step 20 bp. C. L segment, window 400 bp, step 50 bp.
Mentions: Recombination within CCHFV genome segments was reported previously [17] and confirmed in subsequent studies [3]. CCHFV sequences were analyzed for recombination using the RDP 4.0 package, which utilizes a panel of algorithms. The detected cases were then visualized using bootscan graphs. Consistent with previous reports, several cases of significantly supported recombination events were found within the S segment (Fig 4A and 4B). In the L segment, only GtII (M-I) viruses isolated in DRC and Uganda displayed evidence of recombination. Interestingly, the pattern was highly mosaic and implied multiple exchanges within that group (Fig 4C). These recombination events were identified in the middle of individual chromatograms of the Nakiwogo strain sequenced in this work, ruling out experimental error (amplification of fragments of different genomes from a mixture of viruses). No reliably supported recombination events could be detected in the M segment; however, a few sequences had evidence of introduction of very short highly divergent sequences of unknown origin, suggestive of sequencing errors. In general, in CCHFV there were significantly fewer suggested recombination events than reassortment cases.

View Article: PubMed Central - PubMed

ABSTRACT

Crimean Congo hemorrhagic fever virus (CCHFV) is one of the most severe viral zoonozes. It is prevalent throughout Africa, Asia and southern Europe. Limited availability of sequence data has hindered phylogeographic studies. The complete genomic sequence of all three segments of 14 Crimean Congo hemorrhagic fever virus strains isolated from 1958–2000 in Russia, Central Asia and Africa was identified. Each genomic segment was independently subjected to continuous Bayesian phylogeographic analysis. The origin of each genomic segment was traced to Africa about 1,000–5,000 years ago. The virus was first introduced to South and Central Asia in the Middle Ages, and then spread to China, India and Russia. Reverse transfers of genomic segments from Asia to Africa were also observed. The European CCHFV genotype V was introduced to Europe via the Astrakhan region in South Russia 280–400 years ago and subsequently gradually spread westward in Russia, to Turkey and the Balkans less than 150 years ago. Only a few recombination events could be suggested in S and L genomic segments, while segment reassortment was very common. The median height of a non-reassortant phylogenetic tree node was 68–156 years. There were reassortment events within the European CCHFV lineage, but not with viruses from other locations. Therefore, CCHFV in Europe is a recently emerged zoonosis that represents a spillover from the global gene pool.

No MeSH data available.


Related in: MedlinePlus