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Home My WebLink AboutCORRESPONDENCE - PURCHASE ORDER - 9153167 (2)Project Proposal (PASS #122684) Testing of Mosquito Pools for West Nile Virus, City of Fort Collins, 2015 BACKGROUND West Nile virus (WNV) first appeared in Colorado in 2002. Since that time, CO, particularly the northern Front Range counties (Larimer, Weld, Boulder), have seen WNV disease cases in humans in every year. Case data for Fort Collins are not available, but it is reasonable to assume that a significant proportion of Larimer County cases occurred in Fort Collins (FC) or Loveland (LV) residents. In Larimer County, the annual number of cases reported has ranged from a high of 546 in 2003 to a low of a single case in 2011, with a total of 859 cases to date (Table 1). This represents 17% of the total cases reported. Larimer County generally reports a disproportionally large percent of all WNV cases in CO. Table 1. Reported West Nile virus infections in humans, 2003-2014, Larimer County and statewide, including severe (neuroinvasive) and fatal case numbers. Data from Colorado Dept. of Health and Environment, as of 04/28/2015 (available on the Internet at: https://www.colorado.gov/pacific/sites/default/files/DC_CD-Zoo-WNV-Report.pdf). Year Larimer County Colorado % of state cases reported by Larimer County County cases Neuro- invasive 1 cases Fatalities State cases Neuro- invasive 1 cases Fatalities 2002 0 0 0 13 0 0 0.0 2003 546 64 10 2,947 622 66 18.5 2004 17 1 0 291 41 4 5.8 2005 13 2 0 106 21 2 12.3 2006 42 7 1 345 65 7 12.2 2007 94 4 0 578 100 7 16.3 2008 13 3 1 71 17 1 18.3 2009 25 10 0 103 35 3 24.3 2010 13 3 0 81 26 4 16.0 2011 1 0 0 7 2 0 14.3 2012 8 3 0 131 62 5 6.1 2013 89 17 1 320 90 7 29.0 2014 18 3 0 114 45 5 15.8 Total 879 117 13 5,107 1,126 111 17.2 1 Includes encephalitis, meningitis, and flaccid paralysis. FC responded to the emergence of WNV in 2003 by establishing a surveillance and control program. The surveillance involves extensive monitoring of potential larval mosquito habitats and weekly collection and testing of adult Culex mosquitoes for WNV. Primary components of the control portion of the program are source reduction, larviciding and public education. Adulticiding is reserved as an option to be used under exceptional levels of WNV activity within FC. Data from the adult trapping and testing program is essential to deciding if, where, and when adulticiding is necessary in FC: adulticiding was conducted in 2003, 2007, in restricted zones in 2012, and city-wide in 2013. From 2003-2008 CDC provided WNV testing of FC mosquito pools at no charge. That service was no longer available beginning in 2009. Colorado State University (CSU) had been conducting studies of WNV along the Front Range, including virus testing. Thus, CSU could provide the testing service previously offered by the CDC at a competitive cost, and has done so successfully from 2009-2013. Resources available at CSU include trained staff and students, laboratory space in the Infectious Diseases Annex (IDA), equipment and reagents to perform RT-PCR detection of WNV, and standard laboratory equipment such as microscopes, freezers, incubators, etc. 1 PROJECT PROPOSAL A. Period of contract The period of this contract shall extend from June 15 to September 30, 2015. The laboratory testing component of the project will take place from June 15 to August 31. Funding will continue until September 30 to permit data analyses and preparation of the final project report. B. Scope of work 1. Work plan a. Mosquito traps are operated weekly by City’s contractor. b. Mosquitoes are identified by contractor staff and Culex females (Culex tarsalis and Culex spp.) are placed in pools of up to 50 individuals, separated by collection site and collection date. CSU will provide the City’s contractor with standard vials to store and transport the mosquito pools (this eliminates the time-consuming task of transferring specimens once they arrive at IDA). c. Contractor delivers the weekly collection of pools to IDA according to an agreed upon schedule –typically early Thursday afternoon. Contractor provides lists of collections and pool numbers, and list of operational/non-operational traps for the week, in MS Excel format via e-mail attachment. d. IDA staff receives specimens and places in appropriate storage/refrigeration to await processing e. IDA staff conducts spot checks to identify mislabeling, missing pools, etc., then processes pools and performs RT- PCR testing f. IDA staff assembles and interprets PCR results. g. Weekly test results are combined with data provided by Contractor (see B.1.c, above) to produce tabular summaries, including comparison to historic patterns of vector and virus activity (see D, below). h. Reports are sent to City of Fort Collins and to other organizations as needed. 2. Deliverables a. Up to 1,000 pools will be tested under the contract. For the amendment up to an additional 500 pools will be tested for a total of 1,500 under the revised contract. b. Test results will be provided to City by 5 PM Monday of each testing week. Equivocal test results may result in delayed reporting, as accuracy is crucial to the surveillance process. i. Specimens must be received by Thursday at 2 PM for results to be available on Monday of the following week. ii. Pools will be processed in order of collection date (earliest collections processed first) unless otherwise requested by the City’s coordinator. iii. To obtain more rapid test results (e.g., when a sudden increase in virus activity is suspected) pools can be accepted early in the week for expedited testing. 3. Staffing a. PI Ebel, with support by Chet Moore as needed, will oversee day-to-day operation of the project, collate and interpret laboratory data, produce reports, and transmit reports to City of Fort Collins and other agencies as appropriate. b. Graduate Research Assistant Murrieta will receive mosquito pools from contractor and prepare specimens according to protocol; perform RT-PCR testing; maintain laboratory notebooks documenting dates and times, pool numbers, results, and other relevant information; prepare summaries of tests; and deliver these results to the PI in a timely fashion. 2 C. Budget The budget covers West Nile virus testing only. It does not include testing for other potential pathogens of human or veterinary importance. Personnel Salary for PI Greg Ebel; 0.26 month (.13 month for amendment) $2,836 $1,418 Salary for GRA Reyes Murrieta; 1.2 month (40% effort for 3 mo)(.6 months. for amendment) $2,292 $1,146 Fringe cost for salaries $885 $443 TOTAL PERSONNEL COST $6,013 $3,007 Supplies Suplies cost for testing 1 pool for WNV = $14*; 1,000 pools, 500 pools for amendment $14,000 $7,000 * See cost breakdown below Indirect Cost (based on 31.3% of the Modified Total Direct Cost) Indirect Cost $6,264 $3,132 TOTAL BUDGET Direct Cost $20,013 $10,007 Indirect Cost $6,264 $3,132 GRAND TOTAL $26,277 $13,139 Breakdown for cost of testing 1 mosquito pool for WNV Procedure Kit/Product Cost Each (Kit/bag) n Cost/ piece # needed/ specimen Total Cost for testing Homogenization Ball Bearings $46.00 100 $0.46 1 $0.46 Homogenization 2mL tubes $53.00 500 $0.11 1 $0.11 RNA extraction MagMax Viral 96 5x $1,200.80 480 $2.50 1 $2.50 RNA extraction Chemicals (EtOH, etc) $0.25 RT-PCR Qiagen One Step $527.00 100 $5.27 1 $5.27 RT-PCR Primers $0.20 Electrophoresis Various (agarose, etbr) $0.25 Pipette Tips Various $3.00 Gloves Various $2.00 Purification 96 KF Plate $145.88 48 $3.04 0.010416667 $0.03 Purification Deep well plate $249.20 50 $4.98 0.010416667 $0.05 Purification KF tip comb $491.03 100 $4.91 0.010416667 $0.05 TOTAL $14.17 3 D. Reporting templates Based on the need to now report data not only for FC citywide but also separately for each of the four zones the city has been divided into for the purpose of WNV surveillance and mosquito control, CSU had to generate a new reporting template. This new reporting template is tailored to provide data relevant to the Level III and IV entomological triggers (see below) for control measures in the “City of Fort Collins Program Response Guidelines to Mosquito Borne Arboviral Activity (July 2008 edition)”. Level III • Vector index > 0.5 and increasing • Culex mosquito populations increasing and at or above historical average for that time period • Mosquito infection rates of > 3.0 per thousand (0.3%) and increasing Level IV • Vector index > 0.75. • Culex mosquito population above historical average for that time period • Sustained mosquito infection rates of > 5.0 per thousand (0.5%) The new reporting format comprises a set of 6 tables to address the current week (1a, 2a, 3a) and to provide seasonal and historical context (1b, 2b, 3b) (see full table formats on following pages) • Table 1a. Vector Index for current week • Table 1b. Vector Index for All Culex by week from June-August • Table 2a. Vector abundance for current week • Table 2b. Vector abundance for All Culex by week from June-August • Table 3a. WNV infection rate per 1,000 females for current week • Table 3b. WNV infection rate per 1,000 females for All Culex by week from June-August Additionally, the weekly reporting will include the MS Excel spreadsheet completed with WNV infection data. 4 Table 1a. Vector Index for current week Week: Mean abundance of females per trap night1 Estimate for proportion of females infected with WNV2 Vector Index Cx. pipiens Cx. tarsalis Cx. pipiens Cx. tarsalis Cx. pipiens3 Cx. tarsalis4 All Culex5 FC – Zone 1 FC – Zone 2 FC – Zone 3 FC – Zone 4 FC – Citywide LV 1From Table 2a (CDC light trap catches only). 2Derived from the data presented in Table 3a for estimated infection rate per 1,000 females (CDC light trap and gravid trap catches combined). 3Vector Index for Cx. pipiens = (Mean abundance of Cx. pipiens females per trap night) x (Estimate for proportion of all Cx. pipiens females infected with WNV). 4Vector Index for Cx. tarsalis = (Mean abundance of Cx. tarsalis females per trap night) x (Estimate for proportion of all Cx. tarsalis females infected with WNV). 5Vector Index for All Culex = (Vector Index for Cx. pipiens) + (Vector Index for Cx. tarsalis). Table 1b. Vector Index for All Culex by week from June-August ek FC – Zone 1 FC – Zone 2 FC – Zone 3 FC – Zone 4 FC – Citywide LV Current year Historical average1 Current year Historical average1 Current year Historical average1 Current year Historical average1 Current year Historical average1 12006-2013 (2003-2005 were excluded due to changes in trap locations from 2006 onwards). Table 2a. Vector abundance for current week (CDC light trap catches only) Week: Total number females collected Number CDC light trap nights Mean abundance of females per CDC light trap night Cx. pipiens Cx. tarsalis All Culex Cx. pipiens1 Cx. tarsalis2 All Culex3 FC – Zone 1 FC – Zone 2 FC – Zone 3 FC – Zone 4 FC – Citywide LV 1 Mean abundance of Cx. pipiens females per CDC light trap night = (Total number Cx. pipiens females collected) / (Number CDC light trap nights). 2 Mean abundance of Cx. tarsalis females per CDC light trap night = (Total number Cx. tarsalis females collected) / (Number CDC light trap nights). 3 Mean abundance of All Culex females per CDC light trap night = (Total number All Culex females collected) / (Number CDC light trap nights). Table 2b. Vector abundance for All Culex by week from June-August ek FC – Zone 1 FC – Zone 2 FC – Zone 3 FC – Zone 4 FC – Citywide LV Current year Historical average1 Current year Historical average1 Current year Historical average1 Current year Historical average1 Current year Historical average1 Table 3a. WNV infection rate per 1,000 females for current week (CDC light trap and gravid trap catches combined) Total number individuals examined Total number pools examined Total number WNV-infected pools Estimate for WNV infection rate per 1,000 females1 Cx. pipiens Cx. tarsalis All Culex Cx. pipiens Cx. tarsalis All Culex Cx. pipiens Cx. tarsalis All Culex Cx. pipiens Cx. tarsalis All Culex Zone 1 Zone 2 Zone 3 Zone 4 Citywide 1Maximum likelihood estimate (MLE) for WNV infection rate per 1,000 females calculated using the CDC PooledInfRate 4.0 plug-in for Excel. Table 3b. WNV infection rate per 1,000 females for All Culex by week from June-August ek FC – Zone 1 FC – Zone 2 FC – Zone 3 FC – Zone 4 FC – Citywide LV Current year Historical average1 Current year Historical average1 Current year Historical average1 Current year Historical E. Reference material Vector Index CDC. 2013. West Nile Virus in the United States: Guidelines for Surveillance, Prevention, and Control. 4th Revision, June 14, 2013. http://www.cdc.gov/westnile/resources/pdfs/wnvguidelines.pdf The Vector Index is described on pages 63-66 (Appendix 2) in this document. VECTOR INDEX To express the arbovirus transmission risk posed by a vector population adequately, information from all three parameters (vector species presence, vector species density, vector species infection rate) must be considered. The Vector Index (VI) combines all three of the parameters quantified through standard mosquito surveillance procedures in a single value. The VI is simply the estimated average number of infected mosquitoes collected per trap night summed for the key vector species in the area. Summing the VI for the key vector species incorporates the contribution of more than one species and recognizes the fact that WNV transmission may involve one or more primary vectors and several accessory or bridge vectors in an area. The Vector Index is expressed as: Maximum likelihood estimate for WNV infection rate per 1,000 females To account for uneven pool sizes (can range from 1-50 mosquitoes), we calculate a maximum likelihood estimate (MLE) for WNV infection rate per 1,000 females using the CDC PooledInfRate 4.0 plug-in for Excel. CDC. 2014. PooledInfRate, version 4.0 http://www.cdc.gov/westnile/resourcepages/mosqSurvSoft.html 8 average1 Current year Historical average1 12006-2013 (2003-2005 were excluded due to changes in trap locations from 2006 onwards). 7 12006-2013 (2003-2005 were excluded due to changes in trap locations from 2006 onwards). 6 5