| 1. |
|
|
| 2. |
|
|
| 3. |
- Cholleti, Harindranath, et al.
(författare)
-
Genetic characterization of a novel picorna-like virus in Culex spp. Mosquitoes from Mozambique
- 2018
-
Ingår i: Virology Journal. - : Springer Science and Business Media LLC. - 1743-422X. ; 15
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Mosquitoes are the potential vectors for a variety of viruses that can cause diseases in the human and animal populations. Viruses in the order Picornavirales infect a broad range of hosts, including mosquitoes. In this study, we aimed to characterize a novel picorna-like virus from the Culex spp. of mosquitoes from the Zambezi Valley of Mozambique.& para;& para;Methods: The extracted RNA from mosquito pools was pre-amplified with the sequence independent single primer amplification (SISPA) method and subjected to high-throughput sequencing using the Ion Torrent platform. Reads that are classified as Iflaviridae, Picornaviridae and Dicistroviridae were assembled by CodonCode Aligner and SPAdes. Gaps between the viral contigs were sequenced by PCR. The genomic ends were analyzed by 5' and 3' RACE PCRs. The ORF was predicted with the NCBI ORF finder. The conserved domains were identified with ClustalW multiple sequence alignment, and a phylogenetic tree was built with MEGA. The presence of the virus in individual mosquito pools was detected by RT-PCR assay.& para;& para;Results: A near full-length viral genome (9740 nt) was obtained in Culex mosquitoes that encoded a complete ORF (3112 aa), named Culex picorna-like virus (CuPV-1). The predicted ORF had 38% similarity to the Hubei picorna-like virus 35. The sequence of the conserved domains, Helicase-Protease-RNA-dependent RNA polymerase, were identified by multiple sequence alignment and found to be at the 3' end, similar to iflaviruses. Phylogenetic analysis of the putative RdRP amino acid sequences indicated that the virus clustered with members of the Iflaviridae family. CuPV-1 was detected in both Culex and Mansonia individual pools with low infection rates.& para;& para;Conclusions: The study reported a highly divergent, near full-length picorna-like virus genome from Culex spp. mosquitoes from Mozambique. The discovery and characterization of novel viruses in mosquitoes is an initial step, which will provide insights into mosquito-virus interaction mechanisms, genetic diversity and evolution.
|
|
| 4. |
- Cholleti, Harindranath, et al.
(författare)
-
Vector-borne viruses and their detection by viral metagenomics
- 2018
-
Ingår i: Infection Ecology & Epidemiology. - : Informa UK Limited. - 2000-8686. ; 8
-
Forskningsöversikt (refereegranskat)abstract
- Arthropods, such as mosquitoes and ticks, are important vectors for different viruses (so called vector-borne viruses), some of which cause a significant number of human and animal deaths every year as well as affect public health worldwide. Dengue virus, yellow fever virus, chikungunya virus, Japanese encephalitis virus, tick-borne encephalitis virus and Zika virus are just a few examples of important vector-borne viruses. The majority of all vector-borne viruses have an RNA genome, which routinely undergo genetic modifications. The changes in the genome, apart from the environmental issues, can also influence the spread of viruses to new habitats and hosts and lead to the emergence of novel viruses, which may become a threat to public health. Therefore, it is important to investigate the viruses circulating in arthropod vectors to understand their diversity, host range and evolutionary history as well as to predict new emerging pathogens. The choice of detection method is important, as most of the methods can only detect viruses that have been previously well described. Viral metagenomics is a useful tool to simultaneously identify all the viruses present in a sample, including novel viruses. This review describes vector-borne viruses, their maintenance and emergence in nature, and detection using viral metagenomics.
|
|
| 5. |
- Cholleti, Harindranath, et al.
(författare)
-
Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique
- 2018
-
Ingår i: Infection Ecology & Epidemiology. - : Informa UK Limited. - 2000-8686. ; 8
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Ticks are primary vectors for many well-known disease-causing agents that affect human and animal populations globally such as tick-borne encephalitis, CrimeanCongo hemorrhagic fever and African swine fever. In this study, viral metagenomics was used to identify what viruses are present in Rhipicephalus spp. ticks collected in the Zambezi Valley of Mozambique. Methods: The RNA was amplified with sequence-independent single primer amplification (SISPA) and high-throughput sequencing was performed on the Ion Torrent platform. The generated sequences were subjected to quality check and classfied by BLAST. CodonCode aligner and SeqMan were used to assemble the sequences. Results: The majority of viral sequences showed closest sequence identity to the Orthomyxoviridae family, although viruses similar to the Parvoviridae and Coronaviridae were also identified. Nearly complete sequences of five orthomyxoviral segments (HA, NP, PB1, PB2, and PA) were obtained and these showed an amino acid identity of 32–52% to known quaranjaviruses. The sequences were most closely related to the Wellfleet Bay virus, detected and isolated from common eider during a mortality event in the USA. Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Further genetic and biological studies are needed in order to investigate potential pathogenesis of the identified orthomyxovirus.
|
|
| 6. |
- Engel, Philipp, et al.
(författare)
-
The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions
- 2016
-
Ingår i: mBio. - : American Society for Microbiology. - 2161-2129 .- 2150-7511. ; 7:2
-
Forskningsöversikt (refereegranskat)abstract
- As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the micro biome. The bee micro biome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee micro biome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.
|
|
| 7. |
|
|
| 8. |
- Gourlé, Hadrien, et al.
(författare)
-
Simulating Illumina metagenomic data with InSilicoSeq
- 2019
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 35, s. 521-522
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation: The accurate in silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented. In this article, we describe InSilicoSeq, a software package to simulate metagenomic Illumina sequencing data. InsilicoSeq has a simple command-line interface and extensive documentation.Results: InSilicoSeq is implemented in Python and capable of simulating realistic Illumina (meta) genomic data in a parallel fashion with sensible default parameters.
|
|
| 9. |
- Hayer, Juliette, et al.
(författare)
-
Four novel picornaviruses detected in Magellanic Penguins (Spheniscus magellanicus) in Chile
- 2021
-
Ingår i: Virology. - : Elsevier BV. - 0042-6822 .- 1178-122X. ; 560, s. 116-123
-
Tidskriftsartikel (refereegranskat)abstract
- Members of the Picornaviridae family comprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the family Picornaviridae in healthy Magellanic penguins, a near threatened species. All samples were subsequently screened by RT-PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses. The viruses were distantly related to members of the genera Hepatovirus, Tremovirus, Gruhelivirus and Crahelvirus. Further, they had more than 60% amino acid divergence from other picornaviruses, and therefore likely constitute novel genera. Our results demonstrate the vast undersampling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to hepatoviruses and tremoviruses in the future.
|
|
| 10. |
- Hayer, Juliette, et al.
(författare)
-
Identification and molecular characterization of highly divergent RNA viruses in cattle, Uganda
- 2022
-
Ingår i: Virus Research. - : Elsevier BV. - 0168-1702 .- 1872-7492. ; 313
-
Tidskriftsartikel (refereegranskat)abstract
- The risk for the emergence of novel viral zoonotic diseases in animals and humans in Uganda is high given its geographical location with high biodiversity. We aimed to identify and characterize viruses in 175 blood samples from cattle selected in Uganda using molecular approaches. We identified 8 viral species belonging to 4 families (Flaviviridae, Peribunyaviridae, Reoviridae and Rhabdoviridae) and 6 genera (Hepacivirus, Pestivirus, Orthobunya-virus, Coltivirus, Dinovernavirus and Ephemerovirus). Four viruses were highly divergent and tetantively named Zikole virus (Family: Flaviviridae), Zeboroti virus (Family: Reoviridae), Zebtine virus (Family: Rhabdoviridae) and Kokolu virus (Family: Rhabdoviridae). In addition, Bovine Hepacivirus, Obodhiang virus, Aedes pseudoscutellaris reovirus and Schmallenberg virus were identified for the first time in Ugandan cattle. We report 8 viral species belonging to 4 viral families including divergent ones in the blood of cattle in Uganda. Hence, cattle may be reservoir hosts for likely emergence of novel viruses with pathogenic potential to cause zoonotic diseases in different species with serious public health implications.
|
|
