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PLoS PathogensEcologyPeer-reviewed journal article

Viruses and vectors tied to honey bee colony losses

Zachary S. LamasiD, Frank D. L. RinkevichiD, Andrew Garavito, Allison Shaulis, Dawn L. BoncristianiiD, Elizabeth Hill, Yan Ping CheniD, Jay Daniel EvansiD

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Abstract

Commercial beekeepers in the US reported severe colony losses early in 2025, as colonies were being staged for their critical role in the almond pollination season in California. Average reported losses since the preceding spring exceeded 60%, with substantial variation among operations. Many colonies were still actively collapsing in January, 2025, when pooled and individual samples were collected then screened for levels of known honey bee pathogens and parasites. Deformed wing virus strains A and B, along with Acute bee paralysis virus, were found at unusually high levels, either in pooled colony samples or in individual bees exhibiting shaking behaviors and morbidity. Differences between these two analyses suggest that direct collections of morbid bees provide a superior diagnostic for causal viruses, a suggestion borne out by confirmation of symptoms and morbidity following isolation and new inoculations. Since these viruses are known to be vectored by parasitic Varroa mites, mites from collapsed colonies were in turn screened for resistance to amitraz, a critical miticide used widely by beekeepers. Miticide resistance was found in all collected Varroa, underscoring the urgent need for new control strategies for this parasite. While viruses are a likely end-stage cause of colony death, other stressors such as nutritional stress and agrochemicals may have also played significant roles.

In-depth summary

Claude Opus 5.5 · xhigh effort · 5 Nov 2026 · from the full text of version 1 (1 Jun 2025) · CC0 1.0

During early-2025 US honey bee collapses (>60% losses), dying bees carried high loads of infectious DWV-A, DWV-B, and ABPV, and 100% of screened Varroa mites carried the amitraz-resistance allele.

Commercial US beekeeping operations suffered >60% colony losses (~1.7 million colonies worth $600 million) ahead of the January 2025 California almond pollination season. Because pooled samples from surviving colonies suffer from survivorship bias, pairing diagnostics of actively dying bees with inoculation bioassays and Varroa miticide-resistance genotyping is needed to identify acute drivers.

Key results

  1. ShownPooled samples from surviving colonies showed high prevalence of Deformed wing virus and Acute bee paralysis virus, but pathogen loads did not differ between weak and strong colonies.

    Across 113 pooled samples (72 weak and 41 strong colonies from six commercial operations managing 183,750 peak colonies), median pathogen detections were 5 (IQR = [2]) in both groups with 78% DWV and 72% ABPV prevalence, and no significant difference in overall pathogen load (PERMANOVA F(2,110) = 0.79, R2 = 0.014, p = .663). · Introduction; Pathogen and parasite levels; Figure legends

  2. ShownIndividual symptomatic dying bees carried significantly higher loads of DWV-A and DWV-B than asymptomatic bees, with DWV-B present in every symptomatic bee.

    Comparing 38 symptomatic dying adult bees with 28 asymptomatic control bees showed significantly elevated DWV-A (Mann-Whitney W = 254, p = .0006) and DWV-B (W = 11, p < .0001), with DWV-B detected in 100% of symptomatic bees vs. 0% of asymptomatic controls and no significant effect of beekeeper operation (DWV-A: p = 0.257; DWV-B: p = 0.343). · Pathogen and parasite levels

  3. ShownViral inocula purified from symptomatic field bees replicated in injected pupae and caused rapid, extreme mortality in naive adult honey bees.

    Morbid-bee isolates (CV3 = 8.43 × 10^6 GE/ul DWV-B; CV4 = 2.27 × 10^6 GE/ul DWV-B; CV5 = 3.52 × 10^7 GE/ul ABPV plus DWV-A/B) amplified in pupae at 36 and 60 h and reduced adult survival (N = 272 and N = 172), with CV5 causing 100% mortality at 10^-4 to 10^-7 dilutions and 44% mortality at 10^-8 (~66 million adult bee LD50 equivalents per bee). · Longevity impacts of collected inocula; Infectivity and Induced mortality from viral…; Discussion

  4. ShownAll Varroa destructor mites sampled from collapsed and surviving colonies carried the genetic marker for resistance to the miticide amitraz.

    TaqMan allelic discrimination of the β2-octopamine receptor (Octβ2R) Y215H mutation in 39 individual Varroa mites from 18 colonies across five operations (16 mites from 5 collapsed colonies and 23 mites from 13 live colonies) detected resistance genotypes in 100% of mites. · Screening for genes linked to amitraz resistance…; Amitraz resistance in Varroa mites

Methods, data and reproducibility

During the January 2025 California almond pollination collapse, screened 113 pooled colony samples and 66 individual symptomatic or asymptomatic adult bees across six operations using SYBR Green RT-qPCR. Injected filtered viral inocula from morbid and asymptomatic bees into pupae and naive adult bees for replication and survival bioassays, and genotyped 39 Varroa mites for the Octβ2R Y215H allele via TaqMan.

  • Pooled colony samples and individual symptomatic/asymptomatic adult honey bees screened by RT-qPCR · honey bee (Apis mellifera) and RNA viruses (DWV-A, DWV-B, ABPV) · n = 113 pooled colonies (72 weak, 41 strong) and 66 individual bees
  • Pupal viral amplification and adult honey bee cage longevity bioassays following viral inoculum injection · honey bee (Apis mellifera) · n = 272 injected adult bees (+16 uninjected) in trial 1; 172 in trial 2
  • Varroa destructor mites genotyped for Octβ2R Y215H amitraz resistance · Varroa destructor · n = 39 mites (16 from 5 collapsed, 23 from 13 live colonies) in 5 operations
Methods & tools
qPCR, TaqMan, CFX Maestro, baseR, RStudio, Vegan, MASS, DescTools, lmerTest, survival, survminer, SAS-JMP
Reagents & environment
baseR and RStudio with packages Vegan, MASS, DescTools, lmerTest, survival, survminer, and GGPlot; SAS-JMP version 18; Bio-Rad CFX Maestro
Reproducibility gaps
Individual-level qPCR, survival, and TaqMan genotyping datasets and R analysis scripts are not deposited in a public repository beyond summary supplementary tables.
Limitations (2)
  • The cross-sectional sampling design during active colony collapse in January 2025 could not capture pre-collapse longitudinal pathogen trajectories and was subject to survivorship bias among remaining colonies. · stated by the authors
  • Molecular screening relied on targeted qPCR primers for known honey bee pathogens; unbiased RNA/DNA sequencing for uncharacterized pathogens and chemical screens for hive pesticide residues were still ongoing. · stated by the authors

Read this if you study pollinator pathology, insect vector-borne RNA viruses, miticide resistance in Varroa destructor, or epidemiological sampling of mass mortality events.

Citations
30
FWCI
105.81
Field percentile
top 1%

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