National Baseline Project

Results

The National Bee Virus Baselining Project has now been completed. During this project 1209 hives had bees collected with samples coming proportionally from all states and territories. Eight viruses were tested across 5,769 pools of samples. Massive thanks to the beekeepers who submitted bees, individual results will be provided to the jurisdictions to be shared with those who submitted samples.

Initial results are below, a further detailed report will be shared in the near future.

Following the detection of Varroa destructor in New South Wales in June 2022, there were concerns that these mites may have introduced one or more of the viruses that have an adverse impact on the health and productivity of honey bees. These include viruses in the Deformed Wing complex, Slow Bee Paralysis viruses and Acute Bee Paralysis virus. Both honey bees and mites were initially tested by NSW DPI at Elizabeth Macarthur Agriculture Institute (EMAI) for the exotic viruses of greatest concern. Subsequently, strategic testing was also undertaken to establish the current prevalence of a range of viruses that were considered to either be endemic or there was data indicating that they may be present in Australia. Testing was initially based on real time PCR assays developed at EMAI but nucleic acid sequencing was also undertaken at CSIRO (Canberra) and EMAI. None of the known high-risk viruses were detected. However, sequencing analyses of mites indicated that rhabdoviruses may be present.

There are several rhabdoviruses (Apis mellifera rhabdovirus - AMR) that have been identified in honey bees and Varroa in the last 7-8 years. As these are relatively recent discoveries globally, their significance as pathogens is unknown but there has been a linkage between heavy Varroa infestations and transmission of these viruses. Following the detection of rhabdovirus nucleic acid by sequencing, real time PCR assays to detect two of the genotypes (AMR1 & AMR2) were developed at EMAI. These assays have subsequently been used extensively to test samples collected in NSW, particularly bee and mite samples from hives that were in close proximity to what is believed to be the incursion area. A small number of positive results were obtained from samples collected during the initial investigation. When the affected zone expanded in 2023, further testing was undertaken on bees and mites collected in these newly identified areas. AMR1 & AMR2 were detected in some (but not all) locations. A very high prevalence of infection was detected in mites in some locations.

For the national baseline survey, bees were collected from each state in proportion to the number of bee-keepers. For owners with <2,000 hives, samples of >150 ethanol preserved bees were collected from each of 3 hives. For owners with >2,000 hives, samples of >150 ethanol preserved bees were collected from each of 6 hives. Samples were tested for each of the major exotic viruses and for most of the endemic viruses (or viruses thought to be present in Australia). For each sample, 4 pools of 15 bees were prepared, resulting in a total of 60 bees being tested for each hive sampled. Pool size and the number of pools to be tested from each hive were determined by a combination of the analytical sensitivity of the real time PCR assays and the number of individual bees in a pool. The greater the number of bees in a pool, the greater the chance of detecting a low level of infection, provided the sensitivity of the assay was not significantly affected. Testing of samples from multiple hives in an apiary also provided further insight into the prevalence of infection in an apiary and increased the chances of detecting a low level of virus. In contrast, if a virus was present in a colony, pooling of samples can inflate the apparent level of infection because one strong positive can be detected in a pool of 14 uninfected bees. However, this was a secondary consideration as the objective of the survey was to maximise the likelihood of detecting the presence of an exotic virus.

Testing of the samples collected for the national baseline survey has now been completed. A total of 5769 pools of samples were tested representing 86,535 individual bees. When considered at either a state or national level this testing intensity provides a high level of statistical support for the results obtained. There was no evidence of the major exotic viruses (the Deformed Wing complex, Slow Bee Paralysis viruses and Acute Bee Paralysis virus). Prior to 2025, with the exception of NSW, there was no evidence of the detection of the rhabdoviruses. Samples for the national baseline survey were collected in NSW in late 2023-early 2024. AMR1 and/or AMR2 were only detected in a small number of locations, generally close to the areas where these viruses had been originally detected. AMR1 was detected in less than 1% of pools from NSW. However, when these viruses were detected, the prevalence of infection in individual bees was usually high.

Since 2024 all samples submitted to EMAI for surveillance or diagnostic testing have been tested for the presence of AMR1 and AMR2. Overall, there is an increase in the locations in NSW where these viruses have been detected. Since January 2025 there have also been 12 submissions of samples from Queensland. AMR1 and AMR2 were not detected in any Queensland submissions of bees prior to May 2025. The first positives were detected in bee samples collected on 2 May 2025. Retrospective testing of mites collected soon after the detection of Varroa in Queensland confirmed a high prevalence of AMR. In all instances AMR1 was detected and AMR2 was variably present. There is a strong linkage between the presence of AMR2 in samples infected with AMR1 but the exact mechanism of this association is unclear. At this stage the implications of AMR infections for honey bee health in the largely naiive Australian population is unclear. There is clearly a very high prevalence of AMR1 in mite populations, and based on observations in NSW, given time, a similarly high prevalence of AMR1 is likely to be found in Queensland bees.

For the endemic viruses for which testing was undertaken there was a very high prevalence of Black Queen Cell virus (94.8% of all pools tested were positive), Lake Sinai virus genotypes 1 & 2 (83.9%), Sacbrood virus (82.2%) and Israeli Acute paralysis virus (39.0%). Similar trends were observed in all states although there was greater variability for Israeli Acute paralysis virus, ranging from about 10% for the Northern Territory, South Australia and Western Australia, approximately 40% for New South Wales, Victoria and Tasmania but approximately 70% in Queenland samples.