A novel genetic lineage of Tula orthohantavirus in Altai voles (Microtus obscurus) from Turkey

Polat, Ceylan; Ergünay, Koray; Irmak, Sercan; Erdin, Mert; Brinkmann, Annika; Çetintaş, Ortaç; Çoğal, Muhsin; Sözen, Mustafa; Matur, Ferhat; Nitsche, Andreas; Öktem, İbrahim Mehmet Ali

doi:10.1016/j.meegid.2018.11.015

Cited by 18 publications

(8 citation statements)

References 47 publications

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“…DOBV RNA has been identified in A. flavicollis and A. uralensis in the outbreak region (Oktem et al, ). Recently, DOBV was identified in A. flavicollis in the Thrace Region (near Bulgaria), and TULV RNA was identified in Microtus obscurus in the East Anatolian Region of the country (Polat et al, , ).…”

Section: Discussionmentioning

confidence: 99%

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Dynamics of Puumala hantavirus outbreak in Black Sea Region, Turkey

Çelebi

Öztoprak

Öktem

et al. 2019

Zoonoses and Public Health

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Background Some of the hantavirus species in Euro‐Asia cause haemorrhagic fever with renal syndrome (HFRS) in humans. The first documented human hantavirus infection in Turkey was diagnosed in 2009. This report describes the dynamics of the first hantavirus outbreak that emerged in humans in the Western Black Sea Region of Turkey. Methods All the suspected cases of hantavirus infection were admitted to the Infectious Diseases and Clinical Microbiology Department at the Zonguldak Bülent Ecevit University Hospital in Zonguldak, Turkey. The patients were carefully interviewed, examined and evaluated using routine laboratory tests and hantavirus diagnostic tools. Hantavirus‐reactive antibodies (IgM and IgG) in serum samples were detected via enzyme immune assay (EIA) and immunofluorescence assay (IFA) in the acute and convalescence stages of the disease. The presence of hantavirus ribonucleic acid (RNA) was analysed via reverse transcription polymerase chain reaction (RT‐PCR) in serum and urine samples. A focus reduction neutralization test (FRNT) was performed to confirm specific hantavirus serotypes. In addition, a case–control study was conducted to identify possible risk factors for hantavirus transmission in the outbreak area. A control group was composed of asymptomatic individuals who were seronegative for hantavirus IgM and IgG and living in the outbreak area. Results A total of 55 suspected cases of hantavirus infection were admitted to the inpatient clinic between February and June of 2009. Twenty‐four patients were diagnosed with acute HFRS via EIA or IFA. In 22 of the 24 infected patients, Puumala virus (PUUV) was identified as the causative hantavirus type by detecting IgM in the acute stage and an increase in the IgG level in follow‐up serum samples. PUUV was also verified as the infecting agent by FRNT in two of the 24 cases. Among the 24 laboratory‐confirmed HFRS cases, 21 (87.5%) were males and 3 (12.5%) were females, and the mean age was 45.92 years (standard deviation ± 16.90 years). Almost all these individuals were living in villages or rural areas. The 24 HFRS cases were matched with 26 healthy controls for statistical analyses and according to binary logistic regression analysis, and dealing with rodent control activities in gardens or in annexes of their homes (p = 0.021 and Odds ratio [OR] = 17.11) and being male (p = 0.019 and OR = 22.37) were detected as statistically significant risk factors for hantavirus infection. The most commonly observed clinical complaints were fatigue (95.8%), shivering (91.7%), fever (87.1%), headache (70.8%) and nausea (70.8%). Haemodialysis was required for four patients (16.7%). Except for the first case diagnosed with acute hantavirus infection, no patient died. The mean delay time to hospital admission from initiation of symptoms was 5.3 days, the mean duration of febrile days was 2.6 days, and the mean duration of hospital stay was 8.5 days. Conclusion Hantaviruses are circulating in Turkey and causing sporadic or epidemic infection in humans. Addit...

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Section: Discussionmentioning

confidence: 99%

“…Recently, DOBV was identified in A. flavicollis in the Thrace Region (near Bulgaria), and TULV RNA was identified in Microtus obscurus in the East Anatolian Region of the country (Polat et al, 2019(Polat et al, , 2018.…”

Section: Discussionmentioning

confidence: 99%

Dynamics of Puumala hantavirus outbreak in Black Sea Region, Turkey

Çelebi

Öztoprak

Öktem

et al. 2019

Zoonoses and Public Health

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“…High-throughput sequencing methods have started to remedy this and enabled characterization of virus diversity at unprecedented scales (e.g., [7,8]). Access to entire RNA virus genomes, however, is still challenging particularly for many samples obtained in the field because of technical challenges posed by loss of RNA integrity and low viral loads (e.g., [7,9,10]). Increasing the proportion of virus RNA for sequencing using cell culture is often difficult and may result in genetic variation that is not representative of the natural sample.…”

Section: Introductionmentioning

confidence: 99%

“…The publicly available PUUV genomes and the TULV reference genome were sequenced with classical methods (see below), while only recently was high-throughput sequencing based on shotgun approaches used to generate additional TULV genomes [9,26]. In a study of adaptive evolution between two phylogenetic clades within TULV [26], 12 TULV genomes were assembled from shotgun sequencing data but with very low efficiency (proportion of virus reads between 0.001 and 0.2%).…”

Section: Introductionmentioning

confidence: 99%

Assessing Genome-Wide Diversity in European Hantaviruses through Sequence Capture from Natural Host Samples

Hiltbrunner

Heckel

2020

Viruses

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Research on the ecology and evolution of viruses is often hampered by the limitation of sequence information to short parts of the genomes or single genomes derived from cultures. In this study, we use hybrid sequence capture enrichment in combination with high-throughput sequencing to provide efficient access to full genomes of European hantaviruses from rodent samples obtained in the field. We applied this methodology to Tula (TULV) and Puumala (PUUV) orthohantaviruses for which analyses from natural host samples are typically restricted to partial sequences of their tri-segmented RNA genome. We assembled a total of ten novel hantavirus genomes de novo with very high coverage (on average >99%) and sequencing depth (average >247×). A comparison with partial Sanger sequences indicated an accuracy of >99.9% for the assemblies. An analysis of two common vole (Microtus arvalis) samples infected with two TULV strains each allowed for the de novo assembly of all four TULV genomes. Combining the novel sequences with all available TULV and PUUV genomes revealed very similar patterns of sequence diversity along the genomes, except for remarkably higher diversity in the non-coding region of the S-segment in PUUV. The genomic distribution of polymorphisms in the coding sequence was similar between the species, but differed between the segments with the highest sequence divergence of 0.274 for the M-segment, 0.265 for the S-segment, and 0.248 for the L-segment (overall 0.258). Phylogenetic analyses showed the clustering of genome sequences consistent with their geographic distribution within each species. Genome-wide data yielded extremely high node support values, despite the impact of strong mutational saturation that is expected for hantavirus sequences obtained over large spatial distances. We conclude that genome sequencing based on capture enrichment protocols provides an efficient means for ecological and evolutionary investigations of hantaviruses at an unprecedented completeness and depth.

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“…Asia (Polat et al, 2019). In addition to M. arvalis and M. rossiaemeridionalis, TULV has also been found in multiple species of rodents, e. g. M. subterraneus, M. agrestis, M. gregalis, Arvicola amphibius and Lagurus lagurus (Schmidt-Chanasit et al, 2010).…”

Section: Accepted Manuscriptmentioning

confidence: 99%