Virus Isolation and PCR Sample Analysis Services

Virus Isolation and PCR Sample Analysis Services for USGS, Upper Midwest Water Science Center in Wisconsin

Special Notice of Intent to Award a Sole Source Procurement THIS IS NOT A REQUEST FOR QUOTE. THIS IS A NOTICE OF THE GOVERNMENT'S INTENT TO ISSUE A SOLE SOURCE AWARD. This Notice is to announce that the U.S. Department of the Interior (DOI), U.S. Geological Survey (USGS), Upper Midwest Water Science Center, Madison, WI is proposing to negotiate a contract with California Animal Health & Food Safety Lab System (CAFHS) which operates at the University of California-Davis., on a sole source basis for a base year and with the potential of four (4) option years. This requirement is for avian influenza virus isolation and viral RNA analysis. This requirement will be for a base year with four (4) option years.

The proposed action is for products for which the Government intends to solicit and negotiate with only one source under the authority FAR 13.106-1(b)(1). The reason justifying this sole source procurement is that the Government believes only one responsible source can provide the services that will satisfy the agency's requirement.

The following is a description of services that are required to be performed but not limited to:

The USGS Ecosystems Mission Area along with the Upper Midwest Water Science Center, Ohio-Kentucky-Indiana Water Science Center, and the Central Midwest Water Science Center has optimized a method to recover infectious avian influenza virus from surface water. For this work, samples are collected using the optimized method to filter surface water that will be processed (eluted and concentrated) at the Michigan Bacteriological Research Laboratory (MI-BaRL). Subsequently, this method requires confirmation of recovery, viability, and type of virus via egg inoculation and Polymerase Chain Reaction (PCR) techniques.

Collaboration for analysis and reporting are needed for this study. Samples require egg inoculation, extraction, and PCR analysis. Once samples have been analyzed and data has been reported, the collaborator will participate in interpretation of results and writing a manuscript for publication.

1. Use BSL-2+ facilities certified and approved for all aspects of this work, including handling pathogens. All work with [potential] infectious agents will be carried out in certified biosafety cabinets. Lab must be equipped with incubators, real-time PCR machines, automated nucleic acid extraction machines, and several -80C freezers for storage.

2. Viral RNA will be extracted from all concentrated water samples using the MagMax 1836 on the King Fisher Flex (Thermo Fisher; NVSL-WI-0055) following the NAHLN standard operating procedure (NVSL- SOP-0068 (specific for AI/ND)).

3. Molecular detection of the IAV matrix gene by Real-time Reverse Transcriptase PCR (RRT-PCR; Spackman et al., 2002) will be carried out using the VetMax Gold AIV detection kit.

4. All water samples will be mixed 1:1 with an antibiotics cocktail called 33T (provided by National Veterinary Services Laboratory (NVSL)) and then subjected to virus isolation. Samples will be inoculated into 9- to 11-day old specific pathogen-free embryonated chicken eggs (ECE) as described in CAFHS ¿Egg Inoculation for Avian Virus Isolation¿ (Document IF: 3333). Viral RNA will be extracted from all ECE using the MagMax 1836 on the King Fisher Flex (Thermo Fisher; NVSL-WI-0055) following the NAHLN standard operating procedure (NVSL- SOP-0068 (specific for AI/ND)). Molecular detection of the IAV matrix gene by Real-time Reverse Transcriptase PCR (RRT-PCR; Spackman et al., 2002) will be carried out using the VetMax Gold AIV detection kit.

5. Any viral isolates will be further screened against H5, H7, and 2.3.4.4b H5 primers. Any H5 or H7 isolates that yield a cycle threshold value <40 cycles in these subtype specific assays will be submitted immediately to NVSL for confirmation of pathogenicity. Samples that do not hemagglutinate after one passage will be subjected to a second passage, and procedures for HA assay and PCR followed, as above, as needed. Viral stocks (that are not confirmed to be highly pathogenic H5 or H7 at NVSL) will be stored at -80C.

6. Have positive controls of virus and be able to provide this to the USGS laboratory providing the processing of samples (Michigan Bacteriological Research Laboratory or equivalent).

7. Include appropriate positive and negative controls in all extraction runs. Negative and positive controls from the extraction step will be used, as will an IAV matrix gene transcript positive control (National Veterinary Services Laboratory, Ames, IA, USA).

8. Store samples at -80°C until results have been published.

9. Collaborate on final manuscript by providing analytical methods description and input on interpretation of results.

The NAICS code is 541380 - Testing Laboratories and Services.

This is a sole source notice published for informational purposes only and not a request for competitive quotes. Therefore, no solicitation document exists for this requirement. However, all responsible parties interested in responding to this notice are invited to submit a capability statement by the time and date specified in this notice that provides sufficient details for consideration by the Government, via email to: ldwilliams@usgs.gov.

The determination not to compete the contract based on the responses to this notice is solely within the discretion of the Government. Phone calls will not be accepted in response to this notice. All information submitted should support the offeror's capability to provide the services required and shall be furnished at no cost or obligation to the Government. Responses must be in writing and must provide clear and concise documentation indicating an offeror's bona fide capability to provide these services. Verbal responses are not acceptable and will not be considered. The Government reserves the right to cancel this requirement.