Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt


Sequence (5' to 3') Size Primers (ABC) Sequence (5' to 3') Size Primers (D) Sequence (5' to 3') Size DWV (AB) -F27 CATAGCGAATTACGGTGC DWV (ABC) -F27 CATAGCGAAGTACGGTGC DWV (AB) -B1225 GCCGCCTAGCTTCATC DWV (ABC) -B1215 CCGTAATTCTTCAAGTTCCCA DWV (AB) -F1153 ATTAAAAATGGCCTTTAGTTG DWV (ABC) -F1113 TTTTCAATTTAGTTTTGAATTTGAAGG DWV (D) -F1104 TTTTCAATTTAGTTTTGAATTTGAAGG DWV (AB) -B1806 CTTTTCTAATTCAACTTCACC DWV (ABC) -B1887 GTGGTCAAAACTACATTACTATC DWV (D) -B2403 AGCACTCATCCGCAAGGG DWV (AB) -F1725 GATTACGAGTTAGAGTGTG DWV (ABC) -F1719 AGCAGCGAGAATATGAGTTAG DWV (D) -F2271 AAATGGATCATGCTTTAATTAGTG DWV (AB) -B3095 GCTATTACTTTCCTGTAAATC DWV (ABC) -B3151 CATACTTACGCACCCACC DWV (D) -B3084 AAAACTATTGCTCTCTTGTAAATC DWV (AB) -F3018 GTAGGTTAATTGTAGGTTATG DWV (ABC) -F3018 AGGTAGGTTAATTGTAGGTTATG DWV (AB) -B4329 CAATTCTATAACATTATTTACACG DWV (ABC) -B4329 TTCTAATTCTATAACATTATTTACACG DWV (AB) -F4220 TTTGGGTACAACATCGACC DWV (ABC) -F4226 TACAACATCGTCCGGATCG DWV (AB) -B5668 CACACTGATCCCAATAATC DWV (ABC) -B5722 TTGTAGATGTTTCAACACTCCA DWV (AB) -F5625 ACGTGCGAGTCGTACTC DWV (ABC) -F5670 ACCCGTTATCTGATTATTGGG DWV (D )-F5130 GATTGGGTAAAATTAGCTACAG DWV (AB) -B7295 ACGCAGTTATACCAATTATAC DWV (ABC) -B7295 GTACGCAGTTATACCAATTATAC DWV (D) -B7554 CTTTAGGAAACACCACGCC DWV (AB) -F7243 CCCGTGAAAATGATTCGTG DWV (ABC) -F7243 CCCGTGAAAATGATTCGTG DWV (D) -F7834 GATAGTAACATTGTATTGGTGAC DWV (AB) -B8794 CCGTGAATATAGTGTGAGG DWV (ABC) -B8811 CAAGCATGTATCTTTCAAACAATC DWV (D) -B8765 CTCATTAACTGCGTAGTTGAC DWV (AB) -F8688 GGTAAGCGATGGTTGTTTG DWV (ABC) -F8718 TGCAAGATTCGGGATGTTATC DWV (AB) -B10101 ACTATACTAAAATTAGGACGC 
DWV (ABC) 

Supplementary Table S2: Numerical details of the phylogenetic analyses

Numerical details of the phylogenetic analyses. Shown are the name of the genomic region studied; the Maximum Likelihood estimate for the most likely trees (shown in Figure 1); the number of characters included in the phylogenetic analyses and the number of taxa in the analyses. Abbreviations are: the 5' and 3' Untranslated Regions (UTR); the Lp protein (Lp); capsid proteins (VP) and the Non-Structural proteins. Analyses were conducted separately on the nucleotide (nt) and the amino acid (AA) sequences. Oahu Supplementary Table S3: SRA libraries and samples screened for DWV-D Details of the RNA sequencing libraries screened for the presence of DWV-D, including the year, geographic location and host organism the RNA was isolated from, the presence or not of V. destructor in the region, the sequencing technology used (NGS) and average read length, accession number (if available) of the Small Read Archive (SRA) where the original raw data is stored, the original reference (if available), the total number of raw reads screened, the number of these matching DWV in general, and the number matching uniquely to only DWV-D. 



  




  


Supplementary Figure S1: Amplification and sequencing strategy

Amplification and sequencing strategy for determining the full DWV-D/EBV genome sequence. A genome map of DWV-D, indicating all the major structural and non-structural proteins, is shown together with a ruler in 100 nt intervals. Mapped onto this genome are the eight RT-PCR fragments (A-H) amplified with different sets of primers consensual for DWV-A, DWV-B and/or DWV-C, or specific for DWV-D. Also shown is the year the amplicons were produced and sequenced, as well as the primary sequencing technology used. Fragments in black were amplified successfully on the various occasions, while those in grey could not be amplified with the corresponding primers (Supplementary Table S1). 

Supplementary


Supplementary Table S1: Primers for amplifying DWV strains

Primers used for amplifying and sequencing the DWV-D/EBV genome. Shown are the genome fragment (A-H), the primer names, sequences and product sizes for the three sets of primers developed: those consensual for DWV-A and DWB-B (left); those consensual for DWV-A, DWV-B and DWV-C (middle) and those specific for DWV-D/EBV (right).
Joachim R De Miranda, Nor Chejanovsky Laura E Brettell, Anna K Childers, Anne Dalmon, Ward Deboutte, Dirk C De Graaf, Vincent Doublet, Haftom Gebremedhn, Elke Genersch, Sebastian Gisder, Fredrik Granberg, Nizar J Haddad, Rene Kaden, Robyn Manley, Jelle Matthijnssens, Ivan Meeus, Hussein Migdadi, Meghan O Milbrath, Fanny Mondet, Emily J Remnant, John M K Roberts, Eugene V Ryabov, Noa Sela, Guy Smagghe, Hema Somanathan, Lena Wilfert, Owen N Wright, Stephen J Martin, Brenda V Ball
Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt