Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies

Abstract

Treatment of emerging RNA viruses is hampered by the high mutation and replication rates that enable these viruses to operate as a quasispecies. Declining honey bee populations have been attributed to the ectoparasitic mite Varroa destructor and its affiliation with Deformed Wing Virus (DWV). In the current study we use next-generation sequencing to investigate the DWV quasispecies in an apiary known to suffer from overwintering colony losses. We show that the DWV species complex is made up of three master variants. Our results indicate that a new DWV Type C variant is distinct from the previously described types A and B, but together they form a distinct clade compared with other members of the Iflaviridae. The molecular clock estimation predicts that Type C diverged from the other variants ∼319 years ago. The discovery of a new master variant of DWV has important implications for the positive identification of the true pathogen within global honey bee populations.

Construction and Rescue of a Molecular Clone of Deformed Wing Virus (DWV)

“…However, a 5’-terminal stretch of 10 nucleotides was missing from Kakugo virus (DWV-A, AB070959) and at least 21 nucleotides were missing from all other DWV-A genomes and Varroa destructor virus 1 (DWV-B, AY251269, Fig 2B). A length difference of 14 nucleotides was observed, when comparing DWV-A 1414 (KU847397) to the recently published genomic sequence of DWV-C (ERS657949) [27]. …”

“…Iflaviruses are members of the order Picornavirales with a Picornavirus-like genome organization and particle morphology [14]. DWV is separated into the three master variants DWV-A, -B and -C [27]. Master variant A contains the classical DWV strains [28] and Kakugo virus [29], which are responsible for elevated colony mortality [18].…”

Covert deformed wing virus infections have long-term deleterious effects on honeybee foraging and survival

“…In particular, DWV-infected bees started to forage at an earlier age and showed reduced lifespans and total activity spans than control bees. Finally, next-gen sequencing demonstrated that the DWV strain we used for inoculation belonged to the type B DWB master variant [52], which has recently been found to be an emergent, more virulent strain of the DWV virus [25] that currently appears to be the most common strain in Britain [25]. The fact that our DWV lysate was prepared from a randomly selected sample of bees with overt DWV infection symptoms suggest that this strain is now also common in Continental Europe.…”

“…The amount of DWV injected was estimated at 1.2 Â 10 4 -4.6 Â 10 5 DWV copies per bee, and was aimed at mimicking infection loads reported for bees with covert infections (1.4 Â 10 3 -2.4 Â 10 9 copies per bee, [51]). Based on Illumina ultrahigh throughput sequencing, the DWV strain used for inoculation was determined to belong to the type B DWV master variant [52], which has recently been found to be an emergent, slightly more virulent strain of the DWV virus [25] that is currently also the most common strain in Britain [25] (for details, see the electronic supplementary material).…”

First detection of deformed wing and kakugo viruses in honeybees (Apis mellifera L.) in Egypt by real time-polymerase chain reaction (RT-PCR)

“…In addition, DWV Type C variant is distinct from types A and B. Type C had not recently emerged, but rather is an established DWV variant (Mordecai et al, 2016).…”