Genetic analysis and phylogenetic comparison of Black queen cell virus genotypes

Black queen cell virus detected in Canadian mosquitoes

Black queen cell virus (BQCV) is a ubiquitous honeybee virus and a significant pathogen to queen bee (Apis mellifera) larvae. However, many aspects of the virus remain poorly understood, including the transmission dynamics. In this study, we used next-generation sequencing to identify BQCV in Aedes vexans (n = 4,000) collected in 2019 and 2020 from Manitoba, Canada. We assembled de novo the nearly complete (>96%) genome sequence of the virus, which is the first available from North America and the first report of BQCV being harbored by mosquitoes. Phylogenetic tree reconstructions indicated that the genome had 95.5% sequence similarity to a BQCV isolate from Sweden. Sequences of a potential vector (Varroa destructor) and a microsporidian associated with BQCV (Nosema apis) were not identified in the mosquito samples, however, we did detect sequences of plant origin. We, therefore, hypothesize that the virus was indirectly acquired by mosquitoes foraging at the same nectar sources as honeybees.

First detection of Lake Sinai virus in the Czech Republic: a potential member of a new species

Lake Sinai virus (LSV) is one of over 20 honey bee viruses. Variants of LSV have been classified as members of two officially recognised species, Lake Sinai virus 1 and Lake Sinai virus 2. However, there are currently a limited number of whole-genome sequences, and the genetic variability of the virus indicates that additional species may need to be established. Extracted nucleic acid of 209 honey bee samples was screened by PCR for 11 honey bee viruses. LSV was the third most abundant virus (36.9% of positive samples), after Apis mellifera filamentous virus (72.2%) and deformed wing virus (52.5%). LSV-positive samples were analyzed further by PCR with primers targeting the region encoding the viral RNA-dependent RNA polymerase. Subsequently, the PCR products were sequenced, and the resulting sequences were used for a first round of phylogenetic analysis. Based on those results, several isolates were selected for whole-genome sequencing, and the complete genome sequences were used for additional phylogenetic analysis. The results indicated the presence of at least three genetically distinct groups of LSV in the Czech Republic, the most prevalent one being related to LSV 2 but too dissimilar to be considered a member of the same species. Two sequences of a major LSV strain cluster native to the Czech Republic were determined, representing the first Czech LSV strains published to date.

Recovery and genetic characterization of black queen cell virus

Black queen cell virus (BQCV) is a severe threat to the honeybee (Apis mellifera) worldwide. Although several BQCV strains have been reported in China, the molecular basis for BQCV pathogenicity has not been well understood. Thus, a reverse genetic system of BQCV is required for studying viral replication and its pathogenic mechanism. Here, the complete genome sequence of BQCV was obtained from honeybees using reverse transcription PCR (RT-PCR), namely a BQCV China-GS1 strain (KY741959). Then, a phylogenetic tree was built to analyse the genetic relationships among BQCV strains from different regions. Our results showed that the BQCV China-GS1 contained two ORFs, consistent with the known reference strains, except for the BQCV China-JL1 strain (KP119603). Furthermore, the infectious clone of BQCV was constructed based on BQCV China-GS1 using a low copy vector pACYC177 and gene recombination. Due to the lack of culture cells for bee viruses, we infected the healthy bees with infectious clone of BQCV, and the rescued BQCV resulted in the recovery of recombinant virus, which induced higher mortality than those of the control group. Immune response after inoculated with BQCV further confirmed that the infectious clone of BQCV caused the cellular and humoral immune response of honeybee (A. mellifera). In conclusion, the full nucleotide sequence of BQCV China-GS1 strain was determined, and the infectious clone of BQCV was constructed in this study. These data will improve the understanding of pathogenesis and the host immune responses to viral infection.

Silent threat in honey bee colonies: infection dynamics and molecular epidemiological assessment of black queen cell virus in Turkey

Viruses can have devastating effects and cause epidemics in honey bee (Apis mellifera) colonies. Black queen cell virus (BQCV), which is one of the most common honey bee viruses, affects queen bee larvae and their pupae. This study provides information on the dynamics of BQCV infection in honey bees, using molecular diagnostics to investigate the effects of other pathogens and seasonal patterns that are considered relevant to the epidemiology of BQCV. The results showed a relatively high prevalence of the viruses studied. The prevalence of BQCV, acute bee paralysis virus, and deformed wing virus in worker bees was found to be 90%, 62%, and 84%, respectively. The prevalence of BQCV was 58% in larvae and pupae. Furthermore, the prevalence of Nosema ceranae was 46% in worker bees. Statistical analysis showed possible combined effects of BQCV and other examined viruses in terms of infection dynamics, while BQCV did not show seasonal variation. The BQCV isolates detected in this study were placed in a phylogenetic framework using sequence data from comprehensive sampling in previous studies. The analysis suggested that the Turkish strains of BQCV clustered together with Australian and European strains and consisted of homogeneous populations that had evolved from a common ancestor. This is the first report of BQCV infection dynamics in honey bees in Turkey.

Virion structures and genome delivery of honeybee viruses

The western honeybee is the primary pollinator of numerous food crops. Furthermore, honeybees are essential for ecosystem stability by sustaining the diversity and abundance of wild flowering plants. However, the worldwide population of honeybees is under pressure from environmental stress and pathogens. Viruses from the families Iflaviridae and Dicistroviridae, together with their vector, the parasitic mite Varroa destructor, are the major threat to the world's honeybees. Dicistroviruses and iflaviruses have capsids with icosahedral symmetries. Acidic pH triggers the genome release of both dicistroviruses and iflaviruses. The capsids of iflaviruses expand, whereas those of dicistroviruses remain compact until the genome release. Furthermore, dicistroviruses use inner capsid proteins, whereas iflaviruses employ protruding domains or minor capsid proteins from the virion surface to penetrate membranes and deliver their genomes into the cell cytoplasm. The structural characterization of the infection process opens up possibilities for the development of antiviral compounds.

Development of a multiplex RT-PCR assay for the routine detection of seven RNA viruses in Apis mellifera

Colony losses in apiaries are frequently one of the most important problems in beekeeping. Colony loss is multifactorial with many reported disorders, Colony Collapse Disorder (CCD), is an increasingly recognised phenomenon which is thought to be caused by many pathogens, including viruses. The aim of this study was to develop a multiplex RT-PCR (mRT-PCR) test to obtain faster results in routine diagnostic laboratories for seven crucial bee viruses. Specific primers for seven RNA viruses, including Israeli acute bee paralysis virus (IAPV), deformed wing virus (DWV), sacbrood virus (SBV), acute bee paralysis virus (ABPV), black queen cell virus (BQCV), kashmir bee virus (KBV) and chronic paralysis virus (CBPV), were used for testing procedure. The mRT-PCR assay can amplify seven plasmid DNA fragments from the pooled viral genomes and it was shown to be sensitive because virus copy numbers were detected to be 10⁴ copies/μl when log₁₀ serial dilutions were performed for the optimized mRT- PCR method. It is concluded that, mRT-PCR test can be used in routine analysis because this assay can perform specific, sensitive and reliable results also achieves economic gains and time due to detecting seven viral agents simultaneously.

Multiple Virus Infections in Western Honeybee (Apis mellifera L.) Ejaculate Used for Instrumental Insemination

Instrumental insemination of Apis mellifera L. queens is a widely employed technique used in honeybee breeding that enables the effective control of mating. However, drone semen represents a potential source of honeybee viruses. In this study, 43 semen doses collected from apparently healthy drones, and consequently used in instrumental insemination, were analysed using PCR or RT-PCR to detect the presence of viral genome of 11 honeybee viruses. In 91% of samples, viral infection was detected. The survey revealed genomes of five viruses, namely Deformed wing virus (DWV), Acute bee paralysis virus (ABPV), Black queen cell virus (BQCV), Sacbrood virus (SBV), and A. mellifera filamentous virus (AmFV) in 84%, 19%, 14%, 2%, and 67% of samples, respectively. Single infection (30% of samples) as well as multiple infection (61% of samples) of two, three or four pathogens were also evaluated. To the best of our knowledge, this is the first study describing the presence of the BQCV and SBV genome sequence in drone ejaculate. Phylogenetic analysis of BQCV partial helicase gene sequence revealed the high similarity of nucleotide sequence of described Czech strains, which varied from 91.4% to 99.6%. The findings of our study indicate the possibility of venereal transmission of BQCV and SBV.

Molecular detection of black queen cell virus and Kashmir bee virus in honey

Considering the intensive trading nowadays, the honey from the local market was tested for the presence of the six most common bee viruses. To prove the suitability of honey as a sample for the bee viruses detection, the set of different sample types taken directly from the hives we comparatively tested. The study included 30 samples of domestic and 5 samples of imported honey. Additionally, we tested 40 sets of samples including live bees, dead bees, and the honey taken from four apiaries for the evaluation of honey suitability for the virus detection, Two out of the six most common bee viruses were detected in the samples of honey from the market. Black queen cell virus (BQCV) genome was found in 24 domestic honey samples and Kashmir bee virus (KBV) genome was detected in one sample of imported honey. The nucleotide sequences of 24 BQCV isolates showed the highest identity (86.4%) with strains from Europe at the polyprotein gene, whilst the Serbian isolates between each other showed 98.5% similarity. By comparative testing of the different type of samples, in three out of four apiaries BQCV genome was detected in both bees and honey. Evaluating the suitability of honey for the detection of the viral disease by simultaneous testing of live, dead bees, and honey from the same hive, it was shown that the honey can be successfully used for the detection of BQCV. Since, as of yet, there has been no evidence of KBV circulation in Serbia, after its detection in imported honey, there is a substantial risk of its introduction and consequently the need for its surveillance. Therefore, the programs of bee diseases screening should be included in the regular control procedures for the international trade. In addition to this benefit, honey gives an opportunity to beekeepers for continuous monitoring of bees’ health status.

Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria

Honey bee colonies suffer from various pathogens, including honey bee viruses. About 24 viruses have been reported so far. However, six of them are considered to cause severe infection which inflicts heavy losses on beekeeping. The aim of this study was to investigate incidence of six honey bee viruses: deformed wing virus (DWV), acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV), sacbrood virus (SBV), kashmir bee virus (KBV), and black queen cell virus (BQCV) by a reverse transcription polymerase chain reaction (RT-PCR). A total of 250 adult honey bee samples were obtained from 50 colonies from eight apiaries situated in three different parts of the country (South, North and West Bulgaria). The results showed the highest prevalence of DWV followed by SBV and ABPV, and one case of BQCV. A comparison with homology sequences available in GenBank was performed by phylogenetic analysis, and phylogenetic relationships were discussed in the context of newly described genotypes in the uninvestigated South Eastern region of Europe. In conclusion, the present study has been the first to provide sequencing data and phylogenetics analyses of some honey bee viruses in Bulgaria.

Virion Structure of Black Queen Cell Virus, a Common Honeybee Pathogen

Viral diseases are a major threat to honeybee (Apis mellifera) populations worldwide and therefore an important factor in reliable crop pollination and food security. Black queen cell virus (BQCV) is the etiological agent of a fatal disease of honeybee queen larvae and pupae. The virus belongs to the genus Triatovirus from the family Dicistroviridae, which is part of the order Picornavirales. Here we present a crystal structure of BQCV determined to a resolution of 3.4 Å. The virion is formed by 60 copies of each of the major capsid proteins VP1, VP2, and VP3; however, there is no density corresponding to a 75-residue-long minor capsid protein VP4 encoded by the BQCV genome. We show that the VP4 subunits are present in the crystallized virions that are infectious. This aspect of the BQCV virion is similar to that of the previously characterized triatoma virus and supports the recent establishment of the separate genus Triatovirus within the family Dicistroviridae. The C terminus of VP1 and CD loops of capsid proteins VP1 and VP3 of BQCV form 34-Å-tall finger-like protrusions at the virion surface. The protrusions are larger than those of related dicistroviruses.

IMPORTANCE The western honeybee is the most important pollinator of all, and it is required to sustain the agricultural production and biodiversity of wild flowering plants. However, honeybee populations worldwide are suffering from virus infections that cause colony losses. One of the most common, and least known, honeybee pathogens is black queen cell virus (BQCV), which at high titers causes queen larvae and pupae to turn black and die. Here we present the three-dimensional virion structure of BQCV, determined by X-ray crystallography. The structure of BQCV reveals large protrusions on the virion surface. Capsid protein VP1 of BQCV does not contain a hydrophobic pocket. Therefore, the BQCV virion structure provides evidence that capsid-binding antiviral compounds that can prevent the replication of vertebrate picornaviruses may be ineffective against honeybee virus infections.

Analysis of the complete genome sequence of black queen cell virus JL1 from infected honeybees in China

There are six strains of the complete genomic sequences of black queen cell virus (BQCV) published in the GenBank, including South Africa (AF183905), South Korea (JX149531), Hungary 10 (EF517515), Poland 4 (EF517519), Poland 5 (EF517520) and Poland 6 (EF517521). Based on the six BQCV strains published in the GenBank, ten pairs of primers were designed in the present study using reverse transcription polymerase chain reaction to obtain the first complete genome sequence of a BQCV strain in China, called the BQCV China-JL1 strain (KP119603). A phylogenetic tree was then built to analyse their genetic relationships. The BQCV China-JL1 strain showed 86-93% similarity with the six strains published in the GenBank. The BQCV China-JL1 strain consisted of 8358 nucleotides (nt). The 5'-proximal open reading frame (ORF1) initiated at nt position 546 and terminated at nt position 4676, ORF3 initiated at nt position 4891 and terminated at nt position 5433, and the 3'-proximal ORF (ORF2) was located between nt positions 5750 and 8203.

Capsid Gene Divergence of Black Queen Cell Virus Isolates in Thailand and Japan Honey Bee Species

Black queen cell virus (BQCV) has been found in honey bees worldwide. By using the reverse transcription polymerase chain reaction (RT-PCR) technique, BQCV was detected in a non-native species, Apis mellifera L., collected in both Thailand and Japan, and three other honey bee species (Apis cerana indica F., Apis dorsata F., and Apis florae F.) native to Thailand and Apis cerana japonica F. native to Japan. Based on the capsid coding region, the phylogenetic analysis showed that the BQCV strains found in A. cerana indica and A. cerana japonica were similar within the group and closer to BQCV in Asia. It is interesting to note that the genetic variation of the BQCV isolates was more associated with geographic origin than the host bee species from which the isolates were obtained.

Phylogenetics based on partial ORF2 of triatoma virus in triatomines collected over a decade from domiciliary habitats

The only virus sequenced and studied in triatomines is the Triatoma virus, from the Dicistroviridae family, which causes delayed development, reduced oviposition, and premature death of infected insects. With the goal of expanding the sequences already obtained in previous years and verifying if any changes occurred in their genomic sequences, 68 samples of triatomines from several provinces of Argentina were analyzed. Sixteen positive samples were obtained by Reverse Transcription (RT)-polymerase chain reaction using the VP3-VP1 subregion of open reading frame-2 as a diagnostic method; after sequencing, 11 samples were obtained from Triatoma infestans. These new sequences showed no significant differences in the analyzed regions, which were not grouped by species or habitat or geographical distribution. There were no differences when compared with the sequences found during 2002-2012, all obtained from the wild. We conclude that despite being an RNA virus, the different sequences show high homology.

Analysis of the nonstructural and structural polyprotein regions, and complete genome sequences of Israel acute paralysis viruses identified from honeybees (Apis mellifera) in Korea

Phylogenetic trees were constructed for 24 partial nucleotide sequences of the nonstructural polyprotein (ORF1) and structural polyprotein regions (ORF2) of Korean IAPV genotypes, as well as eight previously reported IAPV sequences from various countries. Most of the Korean genotypes formed a distinct cluster, separate from other country genotypes. To investigate this phenomenon in more detail, three complete IAPV genome sequences were identified from different regions in Korea, i.e., Korea1, Korea2, and Korea3. These sequences were aligned with eight previously reported complete genome sequences and various genome regions were compared. The Korean IAPVs were very similar to those from China and Israel, but highly diverged from USA and Australian genotypes. Interestingly, they showed greater variability than the USA and Australian genotypes in ORF1, but highly similar to the Australian genotype in the ORF2 region. Thus, genetic recombination may account for the spatial distance between the Korean IAPV genotypes and those from other countries.

Phylogenetic analysis of black queen cell virus genotypes in South Korea

The black queen cell virus (BQCV), a picorna-like honeybee virus, was first isolated from queen larvae and pupae of honeybees found dead in their cells. BQCV is the most common cause of death in queen larvae. Phylogenetic analysis of two Apis cerana and three Apis mellifera BQCV genotypes collected from honeybee colonies in different regions of South Korea, central European BQCV genotypes, and a South African BQCV reference genotype was performed on a partial helicase enzyme coding region (ORF1) and a partial structural polypeptide coding region (ORF2). The phylogeny based on the ORF2 region showed clustering of all the Korean genotypes corresponding to their geographic origin, with the exception of Korean Am str3 which showed more similarity to the central European and the South African reference genotype. However, the ORF1-based tree exhibited a different distribution of the Korean strains, in which A. cerana isolates formed one cluster and all A. mellifera isolates formed a separate cluster. The RT-PCR assay described in this study is a sensitive and reliable method for the detection and classification of BQCV strains from various regions of Korea. BQCV infection is present in both A. cerana and A. mellifera colonies. With this in mind, the present study examined the transmission of honeybee BQCV infections between A. cerana and A. mellifera.

New Triatoma virus hosts in wild habitats of Argentina

Triatoma virus (TrV), a member of the Dicistroviridae family, replicates in intestinal epithelial cells, causing delayed development and death of infected individuals. The aims of this study were to find naturally infected species of Triatominae in the wild in the region endemic for Chagas disease and analyze and compare the sequence diversity of TrV obtained from different Triatominae. A total of 253 Triatominae belonging to 10 species were captured by active or passive collection. Three new sequences were obtained from Triatoma infestans, Triatoma delpontei and Psammolestes coreodes and the analysis revealed that these sequences were very similar. Ps. coreodes is a new host for TrV.

Infestation of Japanese native honey bees by tracheal mite and virus from non-native European honey bees in Japan

Invasion of alien species has been shown to cause detrimental effects on habitats of native species. Insect pollinators represent such examples; the introduction of commercial bumble bee species for crop pollination has resulted in competition for an ecological niche with native species, genetic disturbance caused by mating with native species, and pathogen spillover to native species. The European honey bee, Apis mellifera, was first introduced into Japan for apiculture in 1877, and queen bees have been imported from several countries for many years. However, its effects on Japanese native honey bee, Apis cerana japonica, have never been addressed. We thus conducted the survey of honey bee viruses and Acarapis mites using both A. mellifera and A. c. japonica colonies to examine their infestation in native and non-native honey bee species in Japan. Honey bee viruses, Deformed wing virus (DWV), Black queen cell virus (BQCV), Israeli acute paralysis virus (IAPV), and Sacbrood virus (SBV), were found in both A. mellifera and A. c. japonica colonies; however, the infection frequency of viruses in A. c. japonica was lower than that in A. mellifera colonies. Based on the phylogenies of DWV, BQCV, and SBV isolates from A. mellifera and A. c. japonica, DWV and BQCV may infect both honey bee species; meanwhile, SBV has a clear species barrier. For the first time in Japan, tracheal mite (Acarapis woodi) was specifically found in the dead honey bees from collapsing A. c. japonica colonies. This paper thus provides further evidence that tracheal-mite-infested honey bee colonies can die during cool winters with no other disease present. These results demonstrate the infestation of native honey bees by parasite and pathogens of non-native honey bees that are traded globally.