Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies

Moore, Jonathan D.; Jironkin, Aleksey; Chandler, Dave; Burroughs, Nigel John; Evans, David J.; Ryabov, Eugene V.

doi:10.1099/vir.0.025965-0

Cited by 162 publications

(239 citation statements)

References 23 publications

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“…Specifically, variants of the DWV quasi-species that had VDV-1 capsid proteins and DWV non-capsid proteins prevailed [71]. In 2014, Ryabov along with Moore and colleagues demonstrated that augmentation of DWV titers by Varroa mites is clearly due to facilitation of this specific virulent variant.…”

Section: Experimental Evidence For Virus Infections Causing Death Of mentioning

confidence: 94%

Honey bee colony losses and associated viruses

McMenamin

Genersch

2015

Current Opinion in Insect Science

244

196

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Section: Experimental Evidence For Virus Infections Causing Death Of mentioning

confidence: 94%

Honey bee colony losses and associated viruses

McMenamin

Genersch

2015

Current Opinion in Insect Science

244

196

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“…After trimming adapters and barcodes, the first reads (the reads are paired), 101nts long, were used to calculate the NGS error rate and illustrate the methods. Standard sample: an accurately known mix of two viral recombinants, X59 This was composed of two of the DWV-like viral recombinant RNA genomes described in Moore et al (1992), VDV-1 DV D and VDV-1 VV D (NCBI Accession Nos. HM067437 and HM067438 respectively).…”

Section: Sequence Datamentioning

confidence: 99%

“…HM067437 and HM067438 respectively). The mixture was produced by in vitro RNA transcription using linearized plasmid clones with full-length cDNA inserts of VDV-1 DV D and VDV-1 VV D (Moore et al, 1992) with the T7 mMESSAGEmMACHINE kit (Ambion). The RNA transcripts were purified using RNAeasy columns (Quiagen), quantified, mixed 25% VDV-1 DV D , 75% VDV-1 VV D and sequenced using the Illumina platform protocol.…”

Section: Sequence Datamentioning

confidence: 99%

Error correction and diversity analysis of population mixtures determined by NGS

Wood

Burroughs

Evans

et al. 2014

Preprint

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View the peer-reviewed version (peerj.com/articles/645), which is the preferred citable publication unless you specifically need to cite this preprint.Wood GR, Burroughs NJ, Evans DJ, Ryabov EV. 2014. Error correction and diversity analysis of population mixtures determined by NGS. PeerJ 2:e645 https://doi.org/10.7717/peerj.645 E r r o r c o r r e c t i o n a n d d i v e r s i t y a n a l y s i s o f p o p u l a t i o n mi x t u r e s d e t e r mi n e d b y NGST h e i mp e t u s f o r t h i s wo r k wa s t h e n e e d t o a n a l y s e n u c l e o t i d e d i v e r s i t y i n a v i r a l mi x t a k e n f r o m h o n e y b e e s ; t h e me t h o d s a r e i l l u s t r a t e d u s i n g h o n e y b e e v i r a l s a mp l e s . T h e p a p e r h a s t wo fi n d i n g s . F i r s t , a me t h o d f o r c o r r e c t i o n o f n e x t g e n e r a t i o n s e q u e n c i n g e r r o r i n t h e t o f n u c l e o t i d e d i v e r s i t y i s a s s e mb l e d . A s t a t i s t i c a l l y b a s e d e r r o r c o r r e c t i o n me t h o d i s p r e s e n t e d , wh i c h wo r k s a t t h e l e v e l o f t h e n u c l e o t i d e d i s t r i b u t i o n r a t h e r t h a n t h e l e v e l o f i n d i v i d u a l n u c l e o t i d e s . T h e me t h o d r e l i e s o n a n e r r o r mo d e l a n d a s a mp l e o f k n o wn v i r a l g e n o t y p e s t h a t i s u s e d f o r mo d e l c a l i b r a t i o n . A c o mp e n d i u m o f e x i s t i n g a n d n e w d i v e r s i t y a n a l y s i s t o o l s i s a l s o p r e s e n t e d , a l l o wi n g h y p o t h e s e s a b o u t d i v e r s i t y a n d me a n d i v e r s i t y t o b et e s t e d a n d a s s o c i a t e d c o n fi d e n c e i n t e r v a l s t o b e c a l c u l a t e d . S o f t wa r e i n b o t h E x c e l a n d Ma t l a b a n d a g u i d e a r e a v a i l a b l e a t h t t p : / / www2 . wa r wi c k . a c . u k / f a c / s c i / s y s t e ms b i o l o g y / r e s e a r c h / s o f t wa r e / , t h e Wa r wi c k Un i v e r s i t y S y s t e ms B i o l o g y Ce n t r e s o f t wa r e d o wn l o a d s i t e .P e e r J P r e P r i n t s | h t t p : / / d x . d o i . o r g / 1 0 . 7 2 8 7 / p e e r j . p r e p r i n t s . ABSTRACTThe impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees; the methods are illustrated using honeybee viral samples. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. A statistically based error correction method is presented, which works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated con...

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“…Dodatkowe informacje można znaleźć w pracy Moore i wsp. (11), -opalizujący wirus bezkręgowców (Invertebrate Iridescent Virus; IIV-6) jest wirusem o dwuniciowum DNA z rodziny Iridoviridae. Infekcja IIV-6 skutkuje brakiem aktywności larw i w następstwie ich śmiercią, -wirus mętnych skrzydeł (Cloudy Wing Virus; CWV) to ikozaedralny RNA wirus powodujący zmęt-nienie skrzydeł na skutek krystalicznych struktur wirusowych powstających pomiędzy włóknami mięśni.…”

unclassified

Brief overview of the apian virus taxonomy

Grigorieva¹,

Мatkowska²,

Paleolog³

2016

Medycyna Weterynaryjna

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Klasyfikacja wirusów jest niezwykle elastycznym i zmieniającym się systemem. Wraz z rozwojem wirusologii, w tym wirusologii pszczelej, pojawiają się nowe dane na temat różnych właściwości wirusów, a tym samym sposobu i kryteriów określenia ich miejsca jako patogenów istot żywych. Badacze z Instytutu Doświadczalnej i Klinicznej Medycyny Weterynaryjnej w Charkowie (Ukraina) zajmowali się już tym zagadnieniem (9). W piśmiennictwie świato-wym liczba dostępnych danych wzrasta tak szybko, że wiedzę na ten temat trzeba ciągle aktualizować. Celem tego opracowania była analiza informacji na temat taksonomii wirusów pszczół, tak aby ułatwić czytelnikowi poruszanie się w tym temacie oraz korzystanie z łatwo dostępnych źródeł, szczególnie internetowych, z uwzględnieniem najważniejszych prac przeglądo-wych. W związku z ogólnoświatowym problemem ginięcia i depopulacji rodzin pszczelich zagadnienia wirusowych zakażeń tych owadów znalazły się w centrum uwagi ośrodków zajmujących się biologią, terapią i profilaktyką Apis mellifera i to nie tylko ośrodków stricte pszczelarskich, dlatego adresatami tego artykułu są nie tyle wirusolodzy pszczół, bo tych jest niewielu, ale szerszy krąg naukowców oraz lekarzy weterynarii. W kontekście klasyfikacji taksonomicznej wirusów przeanalizowano w nim informacje z różnych źródeł, zwracając uwagę na strukturę podstawową, kształt, rodzaj genomu, w tym kwasów nukleinowych, wielkość kapsydu i obecność białek. Szczególną uwagę zwrócono na źródła internetowe. Maslii I. G., Matkovska S. G., Paleolog J. Pozycja taksonomiczna wirusów pszczół Brief overview of the apian virus taxonomySummary The aim of this study was to analyze the information on the taxonomy of bee viruses in order to help the reader to navigate throughout this topic. Classification of bee viruses is a changing system. The best known bee viruses belong to the Dicistroviridae and Iflaviridae (Picornavirales; ssRNA +) families. Taxa from the Baculoviridae, Iridoviridae and Poxviridae families should be also considered as potential honeybee pathogens. English researchers have informed about 18 "important bee viruses". 21 different apian virus taxa were blamed, among others, for honeybee losses in US apiaries, including 10 virus taxa considered as the most pathogenic. One of the most comprehensive descriptions of the known bee virus taxa has been provided in the materials of the European COLOSS project. Detailed data from all the above sources were shown in this review. We also analyzed the possibilities of the appearance of some honeybee-parasite viruses, as well as other insect viruses and plant viruses in honeybees. A separate table provides information about the additional publications on the most important taxa of the apian viruses. The crucial role of V. destructor infestation for increased risk of viral infections and, therefore, the urgent need of research on apian virology and on ways of increasing of the honeybee immunity/resistance has been indicated.

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Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies

Cited by 162 publications

References 23 publications

Honey bee colony losses and associated viruses

Honey bee colony losses and associated viruses

Error correction and diversity analysis of population mixtures determined by NGS

Brief overview of the apian virus taxonomy

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