UC Scientists Discover Four New Honey Bee Viruses
June 7, 2011 (Embargo lifts at 2 p.m., June 7, 2011, Pacific Time)
Co-authors of the PLoS recearch include (from left) Michelle Flenniken, a virologist in the Raul Andino lab, Department of Microbiology and Immunology at UC San Francisco and the Häagen-Dazs Honey Bee Postdoctoral Scholar, UC Davis Department of Entomology; professor Joseph DeRisi of the Howard Hughes Medical Institute, and Departments of Medicine, Microbiology, and Biochemistry and Biophysics, UC San Francisco; and Charles Runckel, graduate student in the DeRisi lab. (Photo courtesy of by Mea McNeil)
DAVIS--University of California scientists examining viruses and microbes in healthy commercially managed honey bee colonies over a 10-month period have discovered four new bee viruses, a discovery that may help unlock the secrets of why the bee population is declining.
One virus, the newly named Lake Sinai virus strain 2 (LSV2), predominated. “In fact, we found more than 1 billion LSV2 viral genomes (an approximation of actual viruses) per honey bee in some of the colonies,” said insect virus researcher Michelle Flenniken, a postdoctoral fellow in the Raul Andino lab at UC San Francisco and the recipient of the Häagen-Dazs Postdoctoral Fellowship in Honey Bee Biology at UC Davis.
The virus strain is one of two Lake Sinai strains found among the 431 samples the scientists collected. Both replicate in honey bees, Flenniken said.
Flenniken is part of a seven-member team from the Raul Andino and Joseph DeRisi labs at UC San Francisco that today published “Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia,” in the international Public Library of Science (PLoS) journal.
The research provides “a baseline for future epidemiological studies aimed at understanding current and emerging threats to honey bees and determining the causes of the declining bee population,” Flenniken said.
"Michelle Flenniken is particularly adroit at explaining these findings and techniques to academic audiences and the general public," said Extension apiculturist Eric Mussen of the UC Davis Department of Entomology faculty. Mussen was not involved with the research.
Knowing that numerous viruses, microbes and mites threaten honey bee colony health, the researchers set out to answer the question: “What is normal microbial flora (virus, bacteria, fungi) associated with honey bee colonies over the course of a year?”
They used cutting-edge technology to document the seasonal incidence and abundance of previously characterized viruses. Their broad-scale analysis incorporated a suite of molecular tools: custom microarray, polymerase chain reaction (PCR), quantitative PCR (qPCR) and deep sequencing. Their work enabled rapid detection of the presence—or absence—of all previously identified honey bee pathogens and facilitated the detection of the four novel pathogens.
The scientists performed pathogen screening using the “Arthropod Pathogen Microarray” (APM), a custom DNA microarray capable of detecting more than 200 arthropod associated viruses, microbes, and metazoans. In design principles, it is similar to human pathogen microarray screening.
The APM’s design couples highly conserved nucleic acid targets with hybridization-based detection to identify previously uncharacterized organisms, the scientists said. Endpoint PCR provided sensitive detection while qPCR documented abundance of select pathogens.
These arrays were custom printed and made in UCSF’s Center for Advanced Technology (CAT) facility, located on the second floor of Genentech Hall.
Honey bee is besieged by viruses. This bee is nectaring lavender. (Photo by Kathy Keatley Garvey)
By thoroughly sequencing the nucleic acid in select samples, they discovered four new viruses, two of which were the most abundant honey bee viruses monitored in this 431-sample study.
This result illustrates the power of ultra deep sequencing for viral discovery and broadens the spectrum of potential disease causing agents in honey bees, they said.
Michelle Flenniken, a postdoc in Raul Andino’s lab, and Charles Runckel, a graduate student in the DeRisi lab, were co-first authors, contributing equally to this work. Additional authors include: J. Graham Ruby, postdoctoral fellow in the DeRisi lab; Juan Engel, microscopy core director of the Sandler Center for Drug Discovery and Department of Pathology and Laboratory Medicine; Donald Ganem of the Howard Hughes Medical Institute and Department of Medicine; professor Raul Andino of the Department of Microbiology and Immunology at UCSF and professor Joseph DeRisi of the Howard Hughes Medical Institute, and Departments of Medicine, Microbiology, and Biochemistry and Biophysics at UCSF.
Ultra deep sequencing coupled with a new software, PRICE, developed by J. Graham Ruby in the DeRisi lab (software available at http://derisilab.ucsf.edu/) facilitated the discovery of the four new viruses. Charles Runckel validated the virus sequences using Sanger sequencing. The genomes are publicly accessible in the form of GenBank accessions: Lake Sinai virus strain 1 - HQ871931;Lake Sinai Virus strain 2 -HQ888865; Aphid Lethal Paralysis Virus strain Brookings - Q871932; and Big Sioux River virus- JF423195-8). They also found a trypansomal parasite (Crithidia mellificae), also deposited in public databases so that other researchers can also monitor them.
The research was mainly funded by Project Apis m., (PAm), a Chico-based non-profit organization established in 2006 by beekeepers and orchardists to fund honey bee research on managed colonies. PAm, headed by executive director Christi Heintz, brings together representatives of the American Honey Producers Association (APHA), the American Beekeeping Federation (ABF), the National Honey Board (NHB), California State Beekeepers Association (CSBA), and California almond farmers.
Other financial support: Genentech Graduate Student Fellowship (Runckel); A. P. Giannoni Foundation Medical Research Fellowship and Häagen-Dazs Postdoctoral Fellowship (Flenniken) and the Howard Hughes Medical Institute (DeRisi).
Honey bees pollinate approximately one third of the food in the American diet. Current agricultural practices demand a seasonal abundance of honey bees in geographic locations incapable of maintaining sufficient pollinator populations year-round. Therefore, migratory beekeeping operations transport bees across the U.S. to meet pollination needs. For example, every February, California’s Central Valley requires 1.3 million honey bee colonies (or more than 50 percent of the U.S. mobile honey bee population) for almond pollination. Pollination of all crops (among them, apples, alfalfa and citrus) in the United States is valued at more than $18 billion annually.
The honey bee population has declined since 2006, when a Pennsylvania migratory beekeeper overwintering his bees in Florida reported the first case of what is now known as colony collapse disorder (CCD), a mysterious phenomenon characterized by adult bees abandoning the hive and leaving behind the queen bee, food stores and brood. CCD is associated with increased pathogen incidence.--Kathy Keatley Garvey
Michelle Flenniken Named Häagen-Dazs Postdoctoral Fellow (Aug 6, 2008)
Understanding Honey Bee Immune System Crucial to Battling Declining Honey Bee Population (May 26, 2011)
PLOS Paper: Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia (June 7, 2011)
--Kathy Keatley Garvey
UC Davis Department of Entomology