High-throughput sequencing of two European strains of tick-borne encephalitis virus (TBEV), Hochosterwitz and 1993/783

Paulsen, Katrine Mørk; Lamsal, Alaka; Bastakoti, Srijana; Pettersson, John H.‐O.; Pedersen, Benedikte Nevjen; Stiasny, Karin; Haglund, Mats; Smura, Teemu; Vapalahti, Olli; Vikse, Rose; Alfsnes, Kristian; Andreassen, Åshild Kristine

doi:10.1016/j.ttbdis.2020.101557

Cited by 10 publications

(6 citation statements)

References 49 publications

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“…In specific, whole-genome sequences from Dronten, Zeist, and Hellendoorn were more closely related to strains from Germany, Sweden, and England, respectively, than to each other. These findings are in line with other studies from elsewhere in Europe, which also found high genetic diversity among local TBEV strains in relatively small geographic areas ( 25 – 28 ). For example, TBEV isolates from southwestern Germany were closely related to strains from the Czech Republic, Austria, Switzerland, Slovakia, and Italy ( 28 ).…”

Section: Discussionsupporting

confidence: 93%

“…The diversity of TBEV variants in both the Netherlands and England points toward multiple introduction events in both countries, possibly through migratory birds ( 31 ). Migratory birds have been implicated in the spread of TBEV before ( 25 , 29 , 32 ). However, additional whole-genome sequences are needed from other TBEV risk areas from Europe for a more complete phylogenetic and phylogeographic analysis to determine the mechanisms of spread of the virus.…”

Section: Discussionmentioning

confidence: 99%

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Continued Circulation of Tick-Borne Encephalitis Virus Variants and Detection of Novel Transmission Foci, the Netherlands

Esser¹,

Lim²,

Vries³

et al. 2022

Emerg. Infect. Dis.

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Tick-borne encephalitis virus (TBEV) is an emerging pathogen that was first detected in ticks and humans in the Netherlands in 2015 (ticks) and 2016 (humans). To learn more about its distribution and prevalence in the Netherlands, we conducted large-scale surveillance in ticks and rodents during August 2018–September 2020. We tested 320 wild rodents and >46,000 ticks from 48 locations considered to be at high risk for TBEV circulation. We found TBEV RNA in 3 rodents (0.9%) and 7 tick pools (minimum infection rate 0.02%) from 5 geographically distinct foci. Phylogenetic analyses indicated that 3 different variants of the TBEV-Eu subtype circulate in the Netherlands, suggesting multiple independent introductions. Combined with recent human cases outside known TBEV hotspots, our data demonstrate that the distribution of TBEV in the Netherlands is more widespread than previously thought.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Continued Circulation of Tick-Borne Encephalitis Virus Variants and Detection of Novel Transmission Foci, the Netherlands

Esser¹,

Lim²,

Vries³

et al. 2022

Emerg. Infect. Dis.

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“…Published primer pairs for TBEV-Eu genome amplification are based on large overlapping amplicons (longer than 2 kb) and were designed for sequencing samples with higher viral loads, which usually requires amplification of the virus in cell lines [31]. Because a viral load above 10 6 copies per ml is rare in the blood of TBEV-infected patients [18], we designed new primers for TBEV with shorter amplicons in the range of 450 bp.…”

Section: Discussionmentioning

confidence: 99%

“…Usually, pre-amplification of the viral genome is required to overcome these challenges. Recently, several amplicon-based methods have been developed for the sequencing of viruses, such as Ebola virus [28], Zika virus [29], West Nile virus [30], TBEV [31], and SARS-CoV-2 (Artic Network). However, the previously described amplicon-based sequencing approach for TBEV is based on large overlapping amplicons (approximately 2 kb) and is designed for samples with high viral loads [31].…”

Section: Introductionmentioning

confidence: 99%

Complete Genome Sequencing of Tick-Borne Encephalitis Virus Directly from Clinical Samples: Comparison of Shotgun Metagenomic and Targeted Amplicon-Based Sequencing

Zakotnik

Knap

Bogovič

et al. 2022

Viruses

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The clinical presentation of tick-borne encephalitis virus (TBEV) infection varies from asymptomatic to severe meningoencephalitis or meningoencephalomyelitis. The TBEV subtype has been suggested as one of the most important risk factors for disease severity, but TBEV genetic characterization is difficult. Infection is usually diagnosed in the post-viremic phase, and so relevant clinical samples of TBEV are extremely rare and, when present, are associated with low viral loads. To date, only two complete TBEV genomes sequenced directly from patient clinical samples are publicly available. The aim of this study was to develop novel protocols for the direct sequencing of the TBEV genome, enabling studies of viral genetic determinants that influence disease severity. We developed a novel oligonucleotide primer scheme for amplification of the complete TBEV genome. The primer set was tested on 21 clinical samples with various viral loads and collected over a 15-year period using the two most common sequencing platforms. The amplicon-based strategy was compared to direct shotgun sequencing. Using the novel primer set, we successfully obtained nearly complete TBEV genomes (>90% of genome) from all clinical samples, including those with extremely low viral loads. Comparison of consensus sequences of the TBEV genome generated using the novel amplicon-based strategy and shotgun sequencing showed no difference. We conclude that the novel primer set is a powerful tool for future studies on genetic determinants of TBEV that influence disease severity and will lead to a better understanding of TBE pathogenesis.

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“…Öland Island along the coast of Kalmar County, is a well‐known bird migration stop (Waldenström et al, 2007) and it could potentially be a hotspot for the dispersal of TBEV‐infected ticks by birds. TBEV isolated from a patient in Kalmar in 1993 has been whole genome sequenced and showed the closest resemblance to the NL/UH strain, isolated from I. ricinus ticks in the Netherlands and the Ljubljana strain, isolated from a patient in Slovenia (Paulsen et al, 2021). This suggests that there is a relationship between the long transport of ticks with TBEV infection and tick/human infection.…”

Section: Discussionmentioning

confidence: 99%

Prevalence of tick‐borne encephalitis virus in questing Ixodes ricinus nymphs in southern Scandinavia and the possible influence of meteorological factors

Lamsal,

Edgar,

Jenkins

et al. 2023

Zoonoses and Public Health

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Ixodes ricinus ticks are Scandinavia's main vector for tick‐borne encephalitis virus (TBEV), which infects many people annually. The aims of the present study were (i) to obtain information on the TBEV prevalence in host‐seeking I. ricinus collected within the Øresund‐Kattegat‐Skagerrak (ØKS) region, which lies in southern Norway, southern Sweden and Denmark; (ii) to analyse whether there are potential spatial patterns in the TBEV prevalence; and (iii) to understand the relationship between TBEV prevalence and meteorological factors in southern Scandinavia. Tick nymphs were collected in 2016, in southern Scandinavia, and screened for TBEV, using pools of 10 nymphs, with RT real‐time PCR, and positive samples were confirmed with pyrosequencing. Spatial autocorrelation and cluster analysis was performed with Global Moran's I and SatScan to test for spatial patterns and potential local clusters of the TBEV pool prevalence at each of the 50 sites. A climatic analysis was made to correlate parameters such as minimum, mean and maximum temperature, relative humidity and saturation deficit with TBEV pool prevalence. The climatic data were acquired from the nearest meteorological stations for 2015 and 2016. This study confirms the presence of TBEV in 12 out of 30 locations in Denmark, where six were from Jutland, three from Zealand and two from Bornholm and Falster counties. In total, five out of nine sites were positive from southern Sweden. TBEV prevalence of 0.7%, 0.5% and 0.5%, in nymphs, was found at three sites along the Oslofjord (two sites) and northern Skåne region (one site), indicating a potential concern for public health. We report an overall estimated TBEV prevalence of 0.1% in questing I. ricinus nymphs in southern Scandinavia with a region‐specific prevalence of 0.1% in Denmark, 0.2% in southern Sweden and 0.1% in southeastern Norway. No evidence of a spatial pattern or local clusters was found in the study region. We found a strong correlation between TBEV prevalence in ticks and relative humidity in Sweden and Norway, which might suggest that humidity has a role in maintaining TBEV prevalence in ticks. TBEV is an emerging tick‐borne pathogen in southern Scandinavia, and we recommend further studies to understand the TBEV transmission potential with changing climate in Scandinavia.

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High-throughput sequencing of two European strains of tick-borne encephalitis virus (TBEV), Hochosterwitz and 1993/783

Cited by 10 publications

References 49 publications

Continued Circulation of Tick-Borne Encephalitis Virus Variants and Detection of Novel Transmission Foci, the Netherlands

Continued Circulation of Tick-Borne Encephalitis Virus Variants and Detection of Novel Transmission Foci, the Netherlands

Complete Genome Sequencing of Tick-Borne Encephalitis Virus Directly from Clinical Samples: Comparison of Shotgun Metagenomic and Targeted Amplicon-Based Sequencing

Prevalence of tick‐borne encephalitis virus in questing Ixodes ricinus nymphs in southern Scandinavia and the possible influence of meteorological factors

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