Genomics and Proteomics of Apis mellifera Filamentous Virus Isolated from Honeybees in China

First detection and prevalence of Apis mellifera filamentous virus in Apis mellifera and Varroa destructor in the Republic of Korea

Apis mellifera filamentous virus (AmFV) is a double-stranded DNA virus that infects Apis mellifera bees. To our knowledge, this is the first comprehensive study aiming to detect and analyse the genetic diversity and prevalence of AmFV in Korean honeybee colonies. Phylogenetic analysis based on baculovirus repeat open reading frame-N gene (Bro-N) sequences revealed that AmFV isolates from the Republic of Korea (ROK) fell into two distinct lineages, with genetic origins in Switzerland and China, with nucleotide similarities of 98.3% and 98.2%, respectively. Our prevalence analysis demonstrated a noteworthy infection rate of AmFV in 545 honeybee colonies, reaching 33.09% in 2022 and increasing to 44.90% by 2023. Intriguingly, we also detected AmFV in Varroa destructor mites, highlighting their potential role as vectors and carriers of AmFV. The presence of AmFV was correlated with an increased infection rate of sacbrood virus, deformed wing virus, Lake Sinai virus 2, black queen cell virus, and Nosema ceranae in honeybee colonies. These findings provide valuable insight into the prevalence and potential transmission mechanisms of AmFV in honeybee colonies in the ROK. The results of this study may be instrumental in the effective management of viral infections in honeybee apiaries.

Apis mellifera filamentous virus from a honey bee gut microbiome survey in Hungary

In Hungary, as part of a nationwide, climatically balanced survey for a next-generation sequencing-based study of the honey bee (Apis mellifera) gut microbiome, repeated sampling was carried out during the honey production season (March and May 2019). Among other findings, the presence of Apis mellifera filamentous virus (AmFV) was detected in all samples, some at very high levels. AmFV-derived reads were more abundant in the March samples than in the May samples. In March, a higher abundance of AmFV-originated reads was identified in samples collected from warmer areas compared to those collected from cooler areas. A lower proportion of AmFV-derived reads were identified in samples collected in March from the wetter areas than those collected from the drier areas. AmFV-read abundance in samples collected in May showed no significant differences between groups based on either environmental temperature or precipitation. The AmFV abundance correlated negatively with Bartonella apihabitans, Bartonella choladocola, and positively with Frischella perrara, Gilliamella apicola, Gilliamella sp. ESL0443, Lactobacillus apis, Lactobacillus kullabergensis, Lactobacillus sp. IBH004. De novo metagenome assembly of four samples resulted in almost the complete AmFV genome. According to phylogenetic analysis based on DNA polymerase, the Hungarian strains are closest to the strain CH-05 isolated in Switzerland.

A novel and diverse family of filamentous DNA viruses associated with parasitic wasps

Large dsDNA viruses from the Naldaviricetes class are currently composed of four viral families infecting insects and/or crustaceans. Since the 1970s, particles described as filamentous viruses (FVs) have been observed by electronic microscopy in several species of Hymenoptera parasitoids but until recently, no genomic data was available. This study provides the first comparative morphological and genomic analysis of these FVs. We analyzed the genomes of seven FVs, six of which were newly obtained, to gain a better understanding of their evolutionary history. We show that these FVs share all genomic features of the Naldaviricetes while encoding five specific core genes that distinguish them from their closest relatives, the Hytrosaviruses. By mining public databases, we show that FVs preferentially infect Hymenoptera with parasitoid lifestyle and that these viruses have been repeatedly integrated into the genome of many insects, particularly Hymenoptera parasitoids, overall suggesting a long-standing specialization of these viruses to parasitic wasps. Finally, we propose a taxonomical revision of the class Naldaviricetes in which FVs related to the Leptopilina boulardi FV constitute a fifth family. We propose to name this new family, Filamentoviridae.

Integrase-associated niche differentiation of endogenous large DNA viruses in crustaceans

IMPORTANCE

Crustacean genomes harbor sequences originating from a family of large DNA viruses called nimaviruses, but it is unclear why they are present. We show that endogenous nimaviruses selectively insert into repetitive sequences within the host genome, and this insertion specificity was correlated with different types of integrases, which are DNA recombination enzymes encoded by the nimaviruses themselves. This suggests that endogenous nimaviruses have colonized various genomic niches through the acquisition of integrases with different insertion specificities. Our results point to a novel survival strategy of endogenous large DNA viruses colonizing the host genomes. These findings may clarify the evolution and spread of nimaviruses in crustaceans and lead to measures to control and prevent the spread of pathogenic nimaviruses in aquaculture settings.

Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus

Background

Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues.

Methods

Short-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly.

Results

At least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with 'Africanized' honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1-100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species.

Discussion

Collectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage.

Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

The accidental endogenization of viral elements within eukaryotic genomes can occasionally provide significant evolutionary benefits, giving rise to their long-term retention, that is, to viral domestication. For instance, in some endoparasitoid wasps (whose immature stages develop inside their hosts), the membrane-fusion property of double-stranded DNA viruses have been repeatedly domesticated following ancestral endogenizations. The endogenized genes provide female wasps with a delivery tool to inject virulence factors that are essential to the developmental success of their offspring. Because all known cases of viral domestication involve endoparasitic wasps, we hypothesized that this lifestyle, relying on a close interaction between individuals, may have promoted the endogenization and domestication of viruses. By analyzing the composition of 124 Hymenoptera genomes, spread over the diversity of this clade and including free-living, ecto, and endoparasitoid species, we tested this hypothesis. Our analysis first revealed that double-stranded DNA viruses, in comparison with other viral genomic structures (ssDNA, dsRNA, ssRNA), are more often endogenized and domesticated (that is, retained by selection) than expected from their estimated abundance in insect viral communities. Second, our analysis indicates that the rate at which dsDNA viruses are endogenized is higher in endoparasitoids than in ectoparasitoids or free-living hymenopterans, which also translates into more frequent events of domestication. Hence, these results are consistent with the hypothesis that the endoparasitoid lifestyle has facilitated the endogenization of dsDNA viruses, in turn, increasing the opportunities of domestications that now play a central role in the biology of many endoparasitoid lineages.

Functional Peroral Infectivity Complex of White Spot Syndrome Virus of Shrimp

White spot syndrome virus (WSSV) is a major cause of disease in shrimp cultures worldwide. The infection process of this large circular double-stranded DNA virus has been well studied, but its entry mechanism remains controversial. The major virion envelope protein VP28 has been implicated in oral and systemic viral infection in shrimp. However, genetic analysis of viral DNA has shown the presence of a few genes related to proteins of per os infectivity factor (PIF) complex in baculoviruses. This complex is essential for the entry of baculoviruses, large terrestrial circular DNA viruses, into the midgut epithelial cells of insect larvae. In this study, we aimed to determine whether a PIF complex exists in WSSV, the components of this complex, whether it functions as an oral infectivity complex in shrimp, and the biochemical properties that contribute to its function in a marine environment. The results revealed a WSSV PIF complex (~720 kDa) comprising at least eight proteins, four of which were not identified as PIF homologs: WSV134, VP124 (WSV216), WSSV021, and WSV136. WSV134 is suggested to be a PIF4 homolog due to predicted structural similarity and amino acid sequence identity. The WSSV PIF complex is resistant to alkali, proteolysis, and high salt, properties that are important for maintaining infectivity in aquatic environments. Oral infection can be neutralized by PIF-specific antibodies but not by VP28-specific antibodies. These results indicate that the WSSV PIF complex is critical for WSSV entry into shrimp; the complex's evolutionary significance is also discussed. IMPORTANCE White spot disease, caused by the white spot syndrome virus (WSSV), is a major scourge in cultured shrimp production facilities worldwide. This disease is only effectively controlled by sanitation. Intervention strategies are urgently needed but are limited by a lack of appropriate targets. Our identification of a per os infectivity factor (PIF) complex, which is pivotal for the entry of WSSV into shrimp, could provide new targets for antibody- or dsRNA-based intervention strategies. In addition, the presence of a PIF complex with at least eight components in WSSV, which is ancestrally related to the PIF complex of invertebrate baculoviruses, suggests that this complex is structurally and functionally conserved in disparate virus taxa.