Phylogeography of Crimean Congo Hemorrhagic Fever Virus

Lukashev, Alexander N.; Klimentov, Alexander S.; Smirnova, S E; Dzagurova, Tamara K.; Drexler, Jan Felix; Gmyl, Anatoly P.

doi:10.1371/journal.pone.0166744

Cited by 47 publications

(42 citation statements)

References 28 publications

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“…Moreover, all virus isolates from humans in Oman and the UAE have had remarkably similar S Segments, apart from the nosocomial outbreak in Dubai in 1979 from an Indian index case [21]. In contrast, several different S segment strains of virus are circulating in Somalia, Iran, and Turkey [9,10,51]. This suggests that the Asia 1 S segment of CCHFV has been in endemic in Oman for more than 20 years.…”

Section: Resultsmentioning

confidence: 99%

Molecular epidemiology and high mortality of Crimean-Congo hemorrhagic fever in Oman: a re-emerging infection

Al-Abri

Hewson

Al-Kindi³

et al. 2018

Preprint

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BackgroundCrimean-Congo hemorrhagic fever (CCHF) is a serious disease with a high fatality rate reported in many countries. The first case of CCHF in Oman was detected in 1995 and serosurveys have suggested widespread infection of humans and livestock throughout the country. MethodologyCases of CCHF reported to the Ministry of Health (MoH) of Oman between 1995 and 2017 were retrospectively reviewed. Diagnosis was confirmed by serology and/or molecular tests in Oman.Stored RNA from recent cases was studied by sequencing the complete open reading frame (ORF) of the viral S segment at Public Health England, enabling phylogenetic comparisons to be made with other S segments of strains obtained from the region. FindingsOf 88 cases of CCHF, 4 were sporadic in 1995 and 1996, then none occurred until 2011. From 2011-2017, incidence has steadily increased and 19 (23.8%) of 80 cases clustered around Eid Al Adha. The median (range) age was 33 (15-68) years and 79 (90%) were male. The major risk for infection was contact with animals and/or butchering in 73/88 (83%) and only one case was related to tick bites alone. Severe cases were over-represented: 64 (72.7%) had a platelet count < 50 x 10 9 /L and 32 (36.4%) died. There was no intrafamilial spread or healthcare-associated infection. The viral S segments from 11 patients presenting in 2013 and 2014 were all grouped in Asia 1 (IV) lineage. Conclusions 3CCHF is well-established throughout Oman, with a single strain of virus present for at least 20 years. Most patients are men involved in animal husbandry and butchery. The high mortality suggests that there is substantial under-diagnosis of milder cases. Preventive measures have been introduced to reduce risks of transmission to animal handlers and butchers and to maintain safety in healthcare settings. Author summaryCrimean-Congo hemorrhagic fever, an often fatal tick-borne viral disease, has made an impact in the Sultanate of Oman-affecting nationals and expatriates alike-for the past 20 years. In this retrospective review of the epidemiology and outcomes of cases in Oman from 1995 to 2017, we identified 4 sporadic cases in 1995 and 1996, then none until 2011, followed by a steady increase until 2017. The mortality rate of 32 of 88 cases (36.4%) is high in comparison to studies from other countries and this could be explained by under-diagnoses of milder cases in the Sultanate.Transmission is commonly associated with animal husbandry and butchering and 88% cases were infected by contact with animals, whereas transmission by tick bite is more commonly recorded in some countries. A proportion of cases (23.8%) were clustered around the Eid-Al-Ahda festival which has, from 2011-2017, occurred in the summer months, which have a higher risk of transmission. This additional risk has been noted and preventive measures have been introduced to reduce the risk of transmission to animal handlers and butchers.

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Section: Resultsmentioning

confidence: 99%

Molecular epidemiology and high mortality of Crimean-Congo hemorrhagic fever in Oman: a re-emerging infection

Al-Abri

Hewson

Al-Kindi³

et al. 2018

Preprint

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“…Deyde et al, 2006; Lukashev et al, 2016). This is an unexpected finding, as the evolutionary pressure of a tick species on CCHFV should shape the necessary adaptations of CCHFV to its particular tick environment, a hypothesis not yet empirically supported.…”

Section: Distribution Emergence and Evolution Of Foci: Tick And Hmentioning

confidence: 99%

The role of ticks in the maintenance and transmission of Crimean-Congo hemorrhagic fever virus: A review of published field and laboratory studies

et al. 2017

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This manuscript is part of a series of reviews that aim to cover published research on Crimean-Congo hemorrhagic fever (CCHF) and its etiological agent, CCHF virus (CCHFV). The virus is maintained and transmitted in a vertical and horizontal transmission cycle involving a variety of wild and domestic vertebrate species that act as amplification hosts, without showing signs of illness. These vertebrates have traditionally been considered reservoirs of CCHFV, but in fact they develop only a transient viremia, while the virus can persist in ticks for their entire lifespan, and can also be transmitted vertically to the next generation. As a result, ticks are now considered to be both the vector and the reservoir for the virus. CCHFV has been detected in a wide range of tick species, but only a few have been proven to be vectors and reservoirs, mainly because most published studies have been performed under a broad variety of conditions, precluding definitive characterization. This article reviews the published literature, summarizes current knowledge of the role of ticks in CCHFV maintenance and transmission and provides guidance for how to fill the knowledge gaps. Special focus is given to existing data on tick species in which vertical passage has been demonstrated under natural or experimental conditions. At the same time, we identify earlier reports that used unreliable methods and perceptions to ascribe a vector role to some species of ticks, and have contributed to confusion regarding viral transmission. We also examine epidemiological pathways of CCHFV circulation and discuss priority areas for future research.

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“…This may be explained at least in part by the use of RNP rather than naked RNA as a transcriptional template (490), which is expected to hamper the template switch and some other mechanisms of formation of chimeric genomes. Nevertheless, true intermolecular recombination in these viruses has continuously been demonstrated (491)(492)(493)(494)(495)(496)(497)(498)(499). The error rate (487) and frequency of intermolecular recombination of viruses with doublestranded RNA genomes are relatively low due to peculiarities of their replicative machinery, but again, instances of natural recombination between them have been reported (500)(501)(502)(503).…”

Section: Negative-strand and Double-stranded Rna Virusesmentioning

confidence: 99%

Emergency Services of Viral RNAs: Repair and Remodeling

Agol

Gmyl

2018

Microbiol Mol Biol Rev

Self Cite

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Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.

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Phylogeography of Crimean Congo Hemorrhagic Fever Virus

Cited by 47 publications

References 28 publications

Molecular epidemiology and high mortality of Crimean-Congo hemorrhagic fever in Oman: a re-emerging infection

Molecular epidemiology and high mortality of Crimean-Congo hemorrhagic fever in Oman: a re-emerging infection

The role of ticks in the maintenance and transmission of Crimean-Congo hemorrhagic fever virus: A review of published field and laboratory studies

Emergency Services of Viral RNAs: Repair and Remodeling

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