Dataset Information

Screening of Eurasian Tundra Reindeer for Viral Sequences by Next-Generation Sequencing.

ABSTRACT: Reindeer husbandry is essential for the livelihood and culture of indigenous people in the Arctic. Parts of the herding areas are also used as pastures for farm animals, facilitating potential transmission of viruses between species. Following the Covid-19 pandemic, viruses circulating in the wild are receiving increased attention, since they might pose a potential threat to human health. Climate change will influence the prevalence of infectious diseases of both humans and animals. The aim of this study was to detect known and previously unknown viruses in Eurasian tundra reindeer. In total, 623 nasal and 477 rectal swab samples were collected from reindeer herds in Fennoscandia, Iceland, and Eastern Russia during 2016-2019. Next-generation sequencing analysis and BLAST-homology searches indicated the presence of viruses of domesticated and wild animals, such as bovine viral diarrhea virus, bovine papillomavirus, alcephaline herpesvirus 1 and 2, deer mastadenovirus B, bovine rotavirus, and roe deer picobirnavirus. Several viral species previously found in reindeer and some novel species were detected, although the clinical relevance of these viruses in reindeer is largely unknown. These results indicate that it should be possible to find emerging viruses of relevance for both human and animal health using reindeer as a sentinel species.

SUBMITTER: Sanchez Romano J

PROVIDER: S-EPMC8296488 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Screening of Eurasian Tundra Reindeer for Viral Sequences by Next-Generation Sequencing.

Sánchez Romano Javier J Omazic Anna A Leijon Mikael M Hagström Åsa Å Tryland Morten M Kantanen Juha J Reilas Tiina T Rockström Ulrika U Fedorov Valery V Albihn Ann A

International journal of environmental research and public health 20210618 12

Reindeer husbandry is essential for the livelihood and culture of indigenous people in the Arctic. Parts of the herding areas are also used as pastures for farm animals, facilitating potential transmission of viruses between species. Following the Covid-19 pandemic, viruses circulating in the wild are receiving increased attention, since they might pose a potential threat to human health. Climate change will influence the prevalence of infectious diseases of both humans and animals. The aim of t ...[more]

PMID: 34207171

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Project description:Background: Previous serological screenings have indicated that Eurasian semi-domesticated tundra reindeer (Rangifer tarandus tarandus) in Finnmark, Northern Norway, are exposed to alphaherpesvirus, gammaherpesvirus and pestivirus. Alphaherpesvirus (i.e., Cervid herpesvirus 2; CvHV2) has been identified as the transmissible component of infectious keratoconjunctivitis (IKC). Limited knowledge exists on the presence and prevalence of virus infections in other herding regions in Norway, which are hosting ~67,000 semi-domesticated reindeer and have contact with other species and populations of wildlife and livestock than those present in Finnmark. Methods: Blood samples (n = 618) were obtained over five winter seasons (2013-2018), from eight different herds representing summer pasture districts in Tana, Lakselv, Tromsø, Lødingen, Hattfjelldal, Fosen, Røros, and Filefjell, distributed from North to South of the reindeer herding regions in Norway. Blood samples were investigated for specific antibodies against five viral pathogen groups, alphaherpesvirus, gammaherpesvirus (viruses in the malignant catarrhal fever group; MCFV), pestivirus, bluetongue virus (BTV), and Schmallenberg virus (SBV), by using commercial multispecies serological tests (ELISA). In addition, swab samples obtained from the nasal mucosal membrane from 486 reindeer were investigated by PCR for parapoxvirus-specific DNA. Results: Antibodies against aphaherpesvirus and MCFV were found in all eight herds, with a total prevalence of 42% (range 21-62%) and 11% (range 2-15%), respectively. Anti-Pestivirus antibodies were detected in five of eight herds, with a total prevalence of 19% (range 0-52%), with two of the herds having a particularly high seroprevalence. Antibodies against BTV or SBV were not detected in any of the animals. Parapoxvirus-specific DNA was detected in two animals representing two different herds in Finnmark. Conclusions: This study confirmed that alphaherpesvirus and MCFV are enzootic throughout the geographical reindeer herding regions in Norway, and that pestivirus is present in most of the herds, with varying seroprevalence. No exposure to BTV and SBV was evident. This study also indicated that semi-domesticated reindeer in Finnmark are exposed to parapoxvirus without disease outbreaks being reported from this region.

Project description:BackgroundWhen compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets.MethodsWe developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7.ResultsSeveral combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness.ConclusionsTrimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects.

Project description:BackgroundMosquito-borne viruses pose a serious threat to humans worldwide. There has been an upsurge in the number of mosquito-borne viruses in Europe, mostly belonging to the families Togaviridae, genus Alphavirus (Sindbis, Chikungunya), Flaviviridae (West Nile, Usutu, Dengue), and Peribunyaviridae, genus Orthobunyavirus, California serogroup (Inkoo, Batai, Tahyna). The principal focus of this study was Inkoo (INKV) and Sindbis (SINV) virus circulating in Norway, Sweden, Finland, and some parts of Russia. These viruses are associated with morbidity in humans. However, there is a knowledge gap regarding reservoirs and transmission. Therefore, we aimed to determine the prevalence of INKV and SINV in blood sucking insects and seroprevalence for INKV in semi-domesticated Eurasian tundra reindeer (Rangifer tarandus tarandus) in Norway.Materials and methodsIn total, 213 pools containing about 25 blood sucking insects (BSI) each and 480 reindeer sera were collected in eight Norwegian reindeer summer pasture districts during 2013-2015. The pools were analysed by RT-PCR to detect INKV and by RT-real-time PCR for SINV. Reindeer sera were analysed for INKV-specific IgG by an Indirect Immunofluorescence Assay (n = 480, IIFA) and a Plaque Reduction Neutralization Test (n = 60, PRNT).ResultsAedes spp. were the most dominant species among the collected BSI. Two of the pools were positive for INKV-RNA by RT-PCR and were confirmed by pyrosequencing. The overall estimated pool prevalence (EPP) of INKV in Norway was 0.04%. None of the analysed pools were positive for SINV. Overall IgG seroprevalence in reindeer was 62% positive for INKV by IIFA. Of the 60 reindeer sera- analysed by PRNT for INKV, 80% were confirmed positive, and there was no cross-reactivity with the closely related Tahyna virus (TAHV) and Snowshoe hare virus (SSHV).ConclusionThe occurrence and prevalence of INKV in BSI and the high seroprevalence against the virus among semi-domesticated reindeer in Norway indicate that further studies are required for monitoring this virus. SINV was not detected in the BSI in this study, however, human cases of SINV infection are yearly reported from other regions such as Rjukan in south-central Norway. It is therefore essential to monitor both viruses in the human population. Our findings are important to raise awareness regarding the geographical distribution of these mosquito-borne viruses in Northern Europe.

Dataset Information

Screening of Eurasian Tundra Reindeer for Viral Sequences by Next-Generation Sequencing.

Publications

Screening of Eurasian Tundra Reindeer for Viral Sequences by Next-Generation Sequencing.

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