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N6264518R0016
Section B - Supplies or Services and Prices
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R&D NMRC Vietnam hospital based study
FFP
Human subject use research is present. No funds will be expended without a HRPO review in place. Determine 1) the prevalence of acute undifferentiated fever hospitalized cases due to rickettsial diseases, scrub typhus, and Q fever and 2) the seroprevalence of antibodies (IgG) against rickettsial, oriential, and coxiella agents among undifferentiated fever patients admitted to 27 hospitals in 26 provinces throughout Vietnam.
FOB: Destination
MILSTRIP: N3239818RCN0006
PURCHASE REQUEST NUMBER: N3239818RCN0006
PSC CD: AN42
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| R&D NMRC Vietnam hospital based study |
FFP
Determine 1) the prevalence of acute undifferentiated fever hospitalized cases due to rickettsial diseases, scrub typhus, and Q fever and 2) the seroprevalence of antibodies (IgG) against rickettsial, oriential, and coxiella agents among undifferentiated fever patients admitted to 27 hospitals in 26 provinces throughout Vietnam.
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| R&D NMRC Vietnam community based study |
FFP
Conduct a 1) cross-sectional study to estimate the seroprevalence of antibodies (IgG) against rickettsial, oriential, and coxiella infections among villagers and pest rodents; 2) to determine the prevalence of rickettsiae, orientiae and coxiellae among ectoparasites from domestic (companion animals and livestock) and small peri-domestic vertebrate pest animals (e.g. rodents, shrews); and trapped free living arthropods (e.g. mites, ticks, lice, and fleas); 3) assess the presence of C. burnetii DNA from vaginal and udder swab samples from domestic ruminants; and 4) to identify associated risk factors for human infections at selected high-risk areas.
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| R&D NMRC Vietnam community based study |
FFP
Conduct a 1) cross-sectional study to estimate the seroprevalence of antibodies (IgG) against rickettsial, oriential, and coxiella infections among villagers and pest rodents; 2) to determine the prevalence of rickettsiae, orientiae and coxiellae among ectoparasites from domestic (companion animals and livestock) and small peri-domestic vertebrate pest animals (e.g. rodents, shrews); and trapped free living arthropods (e.g. mites, ticks, lice, and fleas); 3) assess the presence of C. burnetii DNA from vaginal and udder swab samples from domestic ruminants; and 4) to identify associated risk factors for human infections at selected high-risk areas.
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Section C - Descriptions and Specifications
SOW
Naval Medical Research Center Dr. Allen Richards Vietnam Study: rickettsial diseases, scrub typhus and Q fever
Background Rickettsial diseases are seriously under-recognized and under-studied public health problems in Asia. In rural areas they may be the most common treatable cause of fever. Little is known about the prevalence, incidence and distribution of rickettsial diseases, scrub typhus and Q fever in Vietnam. Though there have been some reports in the past, a systematic investigation of rickettsial diseases, scrub typhus and Q fever in Vietnam has not been conducted. Furthermore, Rickettsia prowazekii (epidemic typhus) and Coxiella burnetii (Q fever) are agents that have been weaponized and could be utilized as biological weapons even today. The presence of C. burnetti and R. prowazekii has been reported in neighboring countries, but not in Vietnam. Other Rickettsia species and Orientia tsutsugamushi (scrub typhus) are recognized as important emerging vector-borne infections that are often clinically indistinguishable from the infections caused by R. prowazekii and C. burnetii. Scrub typhus, caused by O. tsutsugamushi, and murine typhus caused by Rickettsia typhi account for up to 30% of malaria-negative fevers nearby in rural Thailand and Laos. In Southeast Asia alone, an estimated 1 million cases of scrub typhus occur yearly, which translates into approx. 50,000 to 80,000 deaths per year. Based on available mortality rates these are almost certainly underestimates, which, together with treatment delays due to lack of awareness and, subsequently, appropriate diagnostics lead to a substantial health and economic impact in the one of the world’s most densely populated regions.
Vietnam is located on the eastern margin of the Indochinese peninsula and occupies about 331,211.6 square kilometers, of which about 25% was under cultivation in 1987. It is a country of tropical lowlands, hills, and densely forested highlands, with level land covering no more than 20% of the area. The northern regions have a humid subtropical climate, with humidity averaging 84% throughout the year. However, because of differences in latitude and the marked variety of topographical relief, the climate tends to vary considerably from place to place. The climate in the southern regions especially Ho Chi Minh City and the surrounding Mekong Delta is predominantly tropical savanna climate with high humidity and a distinct wet and dry season. Vietnam is divided into 8 agro-ecological regions based on topography, climate, soil, and economy including: Northwest, Northeast, Red River Delta, North Central Coast, South Central Coast, Central Highlands, Southeast, and Mekong River Delta. The presence and distribution of the rickettsial pathogens is directly related to the environment, mainly due to their arthropod vectors, and therefore it would be essential to investigate the presence and prevalence of rickettsial diseases (including typhus group [TGR] and spotted fever group [SFGR] rickettsial diseases), scrub typhus, and Q fever, as well as, the vectors that host the causative agents in 8 ecologic regions in 26 provinces throughout Vietnam. Using geographical analyses one could produce a distribution map of rickettsial diseases in Vietnam and also be able to predict areas potentially at risk of rickettsial diseases, scrub typhus, and/or Q fever without surveying the areas. This capability would allow the advancement of the state of epidemiological, laboratory, and environmental science in Vietnam and to identify, reduce and eliminate especially dangerous pathogens and to counter the threat and to mitigate effects of weapons of mass destruction.
Therefore, a project is needed to conduct a 2-year hospital based survey to determine the prevalence and distribution of febrile patients diagnosed with the aforementioned diseases at 27 hospitals in 26 provinces throughout Vietnam. A subsequent follow-on 2-year community based study would be necessarily performed in endemic locations determined from demographic data collected from patients enrolled in the hospitals. Eighty hotspot (high risk areas) within the 8 ecological regions would need to be investigated to determine the presence, identity, prevalence, and distribution of rickettsial diseases, scrub typhus, and Q fever and their etiological agents among people, small vertebrate pests, livestock, and arthropods. Risk maps utilizing GPS/GIS and ecological niche models (ENMs) would be subsequently developed to predict other potential endemic areas in Vietnam. Completing this project would lead to the understanding of the prevalence and distribution of these pathogens in different regions of Vietnam, as well as identifying the ecologic factors associated with their occurrence, essential for the development of prevention and anti-epidemic control measures in the country's public health system.
Proposed Work Timeline (Summary of Tasks)
1. YEARS 1-2: Hospital-based Study Phase Determine 1) the prevalence of acute undifferentiated fever hospitalized cases due to rickettsial diseases, scrub typhus, and Q fever and 2) the seroprevalence of antibodies (IgG) against rickettsial, oriential, and coxiella agents among undifferentiated fever patients admitted to 27 hospitals in 26 provinces throughout Vietnam.
1. YEARS 3-4: Community-based Study Phase Conduct a 1) cross-sectional study to estimate the seroprevalence of antibodies (IgG) against rickettsial, oriential, and coxiella infections among villagers and pest rodents; 2) to determine the prevalence of rickettsiae, orientiae and coxiellae among ectoparasites from domestic (companion animals and livestock) and small peri-domestic vertebrate pest animals (e.g. rodents, shrews); and trapped free living arthropods (e.g. mites, ticks, lice, and fleas); 3) assess the presence of C. burnetii DNA from vaginal and udder swab samples from domestic ruminants; and 4) to identify associated risk factors for human infections at selected high-risk areas.
Tasks and Deliverables
1. Determine the prevalence of acute undifferentiated fever hospitalized cases due to rickettsial diseases, scrub typhus, and Q fever and seroprevalence of rickettsial diseases, scrub typhus, and Q fever among undifferentiated fever patients admitted to 27 hospitals in 26 provinces throughout Vietnam.
0. Year 1 Objectives
0. Year 1 initiates the first year of the entire study, specifically the hospital-based study.
0. Sections 1.3.1 to 1.3.10 and 1.1.12 below apply to the performance requirements of Year 1.
0. The number of samples collected in accordance with Section 1.3.4, will be approximately half of the total expected collections.
0. Section 1.3.10 performance will yield preliminary GIS results.
0. Year 2 Objectives
1. Year 2 is the final year of the hospital-based study and provides the 80 sites that will be needed to start Year 3/community-based portion of the study.
1. Sections 1.3.1-1.3.12 below apply to the performance requirements of Year 2.
1. Sections 1.3.1 to 1.3.3 will be reviewed as necessary (protocols, SOPs, trainings, etc.)
1. The number of samples collected in accordance with Section 1.3.4, will be approximately half of the total expected collections.
1. Section 1.3.10 will yield the final hospital-based GIS results, not the final four-year project GIS results.
0. Work to be Performed During Hospital-based Study:
2. Obtain IRB and Scientific Committee Approval prior to initiation of hospital-based study.
2. Provide Standard Operating Procedures (SOPs) and training as necessary for rickettsial, oriential and coxiella investigations in order to ensure safe and effective implementation of project activities.
2. Develop Data Storage Capability, where data collection formats will be used collaboratively between the scientists and the statistician. Data will be collected by trained study staff via standardized electronic case record forms (eCRFs) using tablets and uploaded to a dedicated central server over 3G or WiFi.
2. Recruit patients (10,000 to 12,000 total in Years 1 and 2) and discuss with hospital management of 3 national hospital and 24 provincial hospitals the proposed project and obtain agreement (Table 1). Provide project overview to personnel involved in study, to include their roles and tasks. Provide GCP and protocol training for hospital personnel involved in study to include: Administrators, Physicians (identify patients to request their enrollment in study, enroll patients, collect eCRF (i.e. patient history and physical examination), and notify study nurse), Study Nurse (collection of consent forms and completed epidemiologic questionnaire, collection of acute samples (i.e. clotted blood, whole EDTA blood for serologic and molecular assays, respectively) before treatment.
Table 1: List of general hospitals selected for investigation of rickettsial diseases, scrub typhus, and Q fever among 26 provinces throughout Vietnam.
| Province/Hospital |
| Ecological region |
| 1 |
| Ha Giang |
| Northeast |
| 2 |
| Cao Bang |
| Northeast |
| 3 |
| PhuTho |
| Northeast |
| 4 |
| Quang Ninh |
| Northeast |
| 5 |
| ThaiNguyen |
| Northeast |
| 6 |
| Lai Châu |
| Northwest |
| 7 |
| Son La |
| Northwest |
| 8 |
| Nam Dinh |
| Red river Delta |
| 9 |
| Hanoi –National Hospital of Tropical Diseases (NHTD) |
| Red river Delta |
| 10 |
| Hai Duong |
| Red river Delta |
| 11 |
| Nghe An |
| North Central Coast |
| 12 |
| Thanh Hoa |
| North Central Coast |
| 13 |
| QuangBinh |
| North Central Coast |
| 14 |
| Hue (National Hospital) |
| North Central Coast |
| 15 |
| Quang Ngai |
| South Central Coast |
| 16 |
| Khanh Hoa |
| South Central Coast |
| 17 |
| Daklak |
| Central Highlands |
| 18 |
| Gia Lai |
| Central Highlands |
| 19 |
| Dong Thap |
| Mekong river Delta |
| 20 |
| Can Tho |
| Mekong river Delta |
| 21 |
| KienGiang |
| Mekong river Delta |
| 22 |
| Bac Lieu |
| Mekong river Delta |
| 23 |
| Binh Phuoc |
| Southeast |
| 24 |
| Ho Chi Minh Hospital of Tropical Diseases (HTD) |
| Southeast |
| 25 |
| Ho Chi Minh - Cho Ray Hospital (National Hospital) |
| Southeast |
| 26 |
| Tay Ninh |
| Southeast |
| 27 |
| Binh Thuan |
| Southeast |
2. Transport all Samples to BSL-2 Laboratory for Serologic and Molecular Analysis and use a professional transport company to transfer these samples. Laboratory testing of study samples will be performed at NHTD and HMU.
2. Perform ELISA on serum samples (acute samples) (n=2,700-4,100) collected from patients.
2. Identify evidence of previous infection with spotted fever group rickettsiae (SFGR), typhus group rickettsiae (TGR), scrub typhus group orientiae (STGO) and Coxiella burnetii IgG ELISAs.
2. Conduct qPCR assays to identify rickettsiae, orientiae, and C. burnetii from DNA extracted from whole blood (EDTA) samples. This will identify active cases of diseases and either genus- or species specific. Use of multilocus sequence typing (MLST) is required if a species-specific qPCR assay is not available to make the agent identification.
2. Combine patient clinical (history and PE), location (GPS of village), serology, and qPCR information/results. Perform data analysis and summarize clinical, epidemiologic and laboratory data. Calculate prevalence of rickettsial diseases, scrub typhus and Q fever among fever patients admitted to 27 hospitals in 26 provinces throughout Vietnam by molecular methods. In addition, calculate prevalence of antibodies to SFGR, TGR, STGO and C. burnetii among fever patients. The acquired data will be entered into CliRes for subsequent analysis by EpiInfo to determine statistical data analysis of pathogen prevalence.
2. Generate GIS maps that will be used to create thematic maps of disease prevalence for the 8 ecological regions of Vietnam for each disease and perform GIS analyses.
1) Northwest Region in the west of Vietnam's northern area contains 4 highland provinces (Lai Chau, Dien Bien, Son La and Hoa Binh); 2 provinces border Laos and 1 borders China.
2) Northeast Region lies to the north of the highly populated Red River lowlands, contains 11 provinces (Cao Bang, Lang Son, BacKan, Thai Nguyen, QuangNinh, BacGiang, Lao Cai, Yen Bai, Ha Giang, TuyenQuang and PhuTho). Many of these provinces are mountainous.
3) Red River Delta Region contains a small but densely populated area that includes 10 provinces along the mouth of the Red River including the capital, Hanoi (Hanoi, HaiPhong, Hai Duong, BacNinh, Hung Yen, Thai Binh, Nam Dinh, Ha Nam, NinhBinh and VinhPhuc).
4) North Central Coast Region in the northern half of Vietnam's narrow central area. All 6 provinces in this region stretch from east coast to Laos in the west (Thanh Hoa, Nghe An, Ha Tinh, QuangBinh, Quang Tri and Hue).
5) South Central Coast Region in the southern half of Vietnam's central area, contains 6 coastal provinces (Da Nang, Quang Nam, QuangNgai, BinhDinh, Phu Yen and Khanh Hoa) and a municipality, Da Nang.
6) Central Highlands Region in south-central Vietnam contains 5 mountainous provinces (Lam Dong, DakNong, Daklak, Gia Lai and Kontum). The ethnic minorities make up the majority of the population.
7) Southeast Region lowland in southern Vietnam contains 8 provinces, plus the municipality of Ho Chi Minh City (Ho Chi Minh, Dong Nai, Binh Duong, BinhPhuoc, TayNinh, NinhThuan, BinhThuan, Vung Tau).
8) Mekong River Delta Region is Vietnam's southernmost region, contains 13 mostly small but populous provinces, plus the municipality of CanThơ (Can Tho, Ben Tre, Dong Thap, SocTrang, Vinh Long, Can Tho, HauGiang, TienGiang, Bac Lieu, Ca Mau, KienGiang, An Giang and TraVinh).
2. Identify10 random villages, towns and/or cities (hotspots) per each of 8 agro-ecological regions (80 sites) based on the demographical information yielded from hospital-based study to investigate the risk for rickettsial diseases, scrub typhus and/or Q fever. For each commune 40 households (approximately 4-5 people/house) should be randomly selected for a cross-sectional study to estimate the seroprevalence of rickettsial diseases, scrub typhus, and Q fever. Total number of villagers to be enrolled for the 8-region IRB approved study should be approximately 16,000.
2. Draft reports and develop presentation(s) for scientific/medical meeting(s) and a manuscript(s) for publication. All data shall be submitted to Principal Investigator Dr. Allen Richards.
0. Activities and Outcomes for this Period of Performance:
3. Report cases of rickettsial diseases, scrub typhus, and Q fever to the Ministry of Health (MoH) and NMRC.
3. Enhance/strengthen provincial clinical diagnosis, treatment and case reporting, laboratory rickettsial diseases, scrub typhus and Q fever diagnosis, and biosafety/biosecurity capacity at provincial hospitals.
0. Deliverables:
| 1.5.1 |
| DELIVERABLE (Summary) |
| DUE |
| 1.5.1.1 |
| Deliverables include a copy of IRB approved study, quarterly status reports of ongoing treatment study and any abstracts and/or manuscripts written for submission to scientific meetings or peer reviewed scientific journals. |
| Quarterly |
| 1.5.1.2 |
| Provide testing results from serological and molecular assays on human specimens. |
| Quarterly |
| 1.5.1.3 |
| Provide generated GIS maps and analyses. |
| Quarterly/Final |
| 1.5.1.4 |
| Provide list of villages for next phase of study. |
| Final |
1.
0.
0.
| The ability to receive/use all samples collected and data generated during the course of the project for at least 12 months after the project end date. |
| Final |
| 1.5.2 |
| DELIVERABLE (Year 1) |
| DUE |
| 1.5.2.1 |
| Present/provide study work plan, IRB approved study protocol and approved SOPs. |
| Work plan, IRB protocol and SOPs will be received prior to start of study; by start of work/first month. |
| 1.5.2.2 |
| Collect hospital-based samples and provide testing results from serological and molecular assays on human specimens. |
| Collection data and associated analysis data will be reported on each enrollee at months 3, 6, 9 and 12. |
| 1.5.2.3 |
| Provide generated GIS maps and analyses. |
| Preliminary distribution map(s) will be generated from tested samples by month 12. |
| 1.5.2.4 |
| Provide technical and progress status reports of ongoing treatment study and any abstracts and/or manuscripts written for submission to scientific meetings or peer reviewed scientific journals. |
| Quarterly and Final |
| 1.5.3 |
| DELIVERABLE (Year 2) |
| DUE |
| 1.5.3.1 |
| Present/provide work plan Year 2; with updated Reviewed IRB protocol and SOPs, if needed |
Work plan, IRB protocol and SOPs will be received prior to start of study; by start of work/first month.
| 1.5.3.2 |
| Collect hospital-based samples and provide testing results from serological and molecular assays on human specimens. |
| Collection data and associated analysis data will be reported on each enrollee at months 3,6, 9 and 12. |
| 1.5.3.3 |
| Provide generated GIS maps and analyses. |
| Distribution map(s) will be generated from tested samples by month 12; results will be included in preliminary map. |
| 1.5.3.4 |
| Identify 10 random villages, towns and /or cities (hotspots) per each of 8 agro-ecological regions for a total of 80 sites based upon demographical information to investigate the risk of rickettsial diseases, scrub typhus and Q fever. For each of the 80 sites select 40 households randomly. |
| End of Year 2. |
| 1.5.3.5 |
| Provide technical and progress status reports of ongoing treatment study and any abstracts and/or manuscripts written for submission to scientific meetings or peer reviewed scientific journals. |
| Quarterly and Final. |
1. Conduct a cross-sectional study to estimate the seroprevalence of rickettsial diseases, scrub typhus, and Q fever among villagers as well as to identify associated risk factors at selected high-risk areas (as described above) to enhance/strengthen surveillance capacity for community-based surveillance for rickettsial diseases, scrub typhus and Q fever, for arthropod vector of human diseases, and for arthropod-borne diseases, as well as, ensure project specimens including serum samples and molecular products are placed in secure repositories at NHTD (human samples) and HMU (animal/arthropod samples).
1. Year 3 Objectives
0. Year 3 Objectives initiate the first year of the community-based study based on the 80 locations identified at the end of Year 2.
0. Sections 2.3.1 to 2.3.5 below apply to the performance requirements of Year 3, where approximately half to two thirds of the expected samples will be collected during first year.
0. For Section 2.3.5, the GIS maps generate will be preliminary for the community-based portion of the study, but can be used to update the Year 1-2 GIS maps.
1. Year 4 Objectives
1. Year 4 Objectives continue the second year of the community-based study and completes the four year project.
1. Sections 2.31-2.3.5 below apply to the performance requirements of Year 4, where implementation of protocols, SOPS, trainings, etc. will be reviewed and approximately one third to half of the expected samples will be collected.
1. For Section 2.3.5, the GIS maps and ENMs generated will be the final versions based on the data collected during the performance year and all four performance years as a whole.
1. Activities and Outcomes for this Period of Performance:
2. Conduct a cross-sectional study to estimate the seroprevalence of rickettsial diseases, scrub typhus, and Q fever among villagers, as well as, to identify associated risk factors at selected high-risk areas (determined in Years 1 and 2) to ascertain the seroprevalence of rickettsioses, scrub typhus and Q fever among healthy villagers and live captured small peri-domestic animals at each study site:
2.3.1.1 Perform the sampling procedure for the cross-sectional study using the sample calculator provided by STEPS provided by the WHO.
2.3.1.2 Develop IRB approved, standardized protocol and questionnaires to recruit villagers from selected communes for collections procedures (to collect demographic information, history of disease, risk factors, and blood samples), as well as, standardized collection procedures for animal and arthropod specimens.
2.2.1.3 Collect sample, demographic & GPS coordinates collection of villagers at 80 sites, to include obtaining signed informed consent forms, conducting interviews with epidemiologic questionnaires, obtaining blood samples from villagers randomly selected, and collecting GPS coordinates. Laboratory testing of study samples will be performed at NHTD.
2.3.1.4 Conduct serological analysis of human blood samples for SFGR, TGR, STGO and C. burnetii.
2.3.1.5 Combine demographic, information on location (GPS) and serologic results to perform data analysis and summarize epidemiologic and serologic data, as well as, calculate prevalence of seroreactivity against TGR, SFGR, STGO and C. burnetii among villagers at 80 sites throughout Vietnam.
Generate GIS maps of seropositivity of villagers across 8 ecological regions of Vietnam for rickettsial diseases, scrub typhus, and/or Q fever using resultant human data in conjunction with coordinate data.
2.3.1.6 Submit reports and develop presentation(s) for scientific/medical meeting(s) and a manuscript(s) for publication. All data shall be submitted to Principal Investigator Dr. Allen Richards.
2.3.2 Ascertain the seroprevalence of rickettsial diseases, scrub typhus, and Q fever among small pest animals live captured at 80 commune sites in high risk areas of 8 ecological regions.
| 2.3.2.1 Select sites to collect live captured small pest animals to obtain blood samples and ectoparasites in different ecological regions. |
| 2.3.2.2 Obtain IACUC approval/exemption to collect swab samples from livestock. |
| 2.3.2.3 Discuss with the Animal Health Center of the provinces and villagers the proposed project and provide training and get approval to collect ectoparasites and other arthropods. |
| 2.3.2.4 Collect ectoparasites and other arthropods, to include blood sampling, host identification and GPS coordinate collection from live capture of small pest animal captured at 80 sites (Tables 2 - 4). Arthropod surveillance efforts in selected areas will focus primarily on peri-domestic pest ectoparasites and ticks, mites, and fleas collected from the environment (e.g. CO2 traps, tick drags/flagging, candle trap and black plate methods). Laboratory testing of study samples will be performed at HMU. |
Table 2. Total number of animal samples estimated per year and for the whole project.
| Animal samples |
| Collection |
Samples/commune Total Samples for 2 years project
| Small peri-domestic animal pests |
| 70-90 |
| 5600-7200 |
Ruminants (vaginal and udder swabs)
| 5-8 |
| 400-640 |
Table 3. The total number of ectoparasites collected from small animal pests estimated for 2 year community-based project (years 3 and 4).
| Samples |
| Collection |
samples/commune Total samples for 2 years project
| ticks from mice |
| 5-10 |
| 400-800 |
| fleas from mice |
| 10-15 |
| 800-1200 |
| mites from mice |
| 35-45 |
| 2800-3600 |
| lice from mice |
| 3-5 |
| 240-400 |
Table 4. The total number of arthropods collected by other methods for 2-year project.
| Samples |
| Collection |
samples/commune Total samples for 2 years project
| ticks |
| 5-10 |
| 400-800 |
| fleas |
| 10-15 |
| 800-1200 |
| mites |
| 35-45 |
| 2800-3600 |
2.3.2.5 Obtain the molecular ID of arthropod-borne rickettsiae, orientiae and C. burnetii by extracting DNA from ticks, mites, fleas and lice, performing qPCR assays specific for rickettsiae, orientiae, and C. burnetii and MLST for Rickettsia sp. identification. Laboratory testing of study samples will be performed at NIMPE.
2.3.2.6 Combine patient clinical information, villager and pest serological data, GPS information on locations, and qPCR/MLST results. Perform data analysis and summarize epidemiologic and serologic data.
2.3.2.7 Draft reports and develop presentation(s) for scientific/medical meeting(s) and a manuscript(s) for publication. All data shall be submitted to Principal Investigator Dr. Allen Richards.
2.3.3 Ascertain the presence, identity, prevalence, and distribution of rickettsia, orientia and Coxiella pathogens in arthropod vectors collected from small animal pests, CO2 traps, tick drags/flags, and black plates at the 80 study sites.
2.3.3.1 Discuss with villagers and get approval to collect ectoparasites and other arthropods at sites described in the Section 2.2.2.
| 2.3.3.2 Collect ectoparasites and other arthropods. |
| 2.3.3.3 Molecular ID the arthropod-borne rickettsiae, orientiae, and C. burnetti. |
| 2.3.3.4 Combine patient clinical information, villager and pest serological data, |
location/GPS information, and qPCR/MLST results to perform data analysis and summarize epidemiologic and serologic data.
2.3.3.5 Draft reports and develop presentation(s) for scientific/medical meeting(s) and a manuscript(s) for publication. All data shall be submitted to Principal Investigator Dr. Allen Richards.
| 2.3.4 Survey livestock for evidence of C. burnetii. | |
| 2.3.4.1 Obtain IACUC approval/exemption to collect swab samples from livestock. | |
| 2.3.4.2 Discuss with villagers and/or farmers to obtain their permission to collect |
samples from their animals and collect animal-associated data will be collected, including: geographical data, age, gender, breed, and other pertinent information.
2.3.4.3 Collect vaginal and udder swabs of livestock in community based study.
Identify livestock and obtain GPS coordinates (Table 2). Swab samples from female domestic livestock (cattle, sheep, or goats) will be collected through the assistance of local veterinarians of the Preventive Medicine Centers of the individual provinces. All samples from domestic livestock will be kept at refrigerated or frozen temperatures as appropriate until tested by molecular assays. Transport all samples (C. burnetii qPCR assay) for analysis.
| 2.3.4.4 Extract DNA from swabs. |
| 2.3.4.5 Conduct C. burnetii specific qPCR assay on extracted DNA samples. |
2.3.4.6 Combine patient clinical information, villager and pest serological data, GIS and location information (i.e. GPS coordinates, households, sheds, and female livestock) and qPCR result to perform data analysis and summarize epidemiologic and serologic data.
2.3.4.7 Draft Draft reports and develop presentation(s) for scientific/medical meeting(s) and a manuscript(s) for publication. All data shall be submitted to Principal Investigator Dr. Allen Richards.
2.3.5 Utilizing GPS coordinates collected at hospitals and field sites, perform GIS and modeling algorithms to develop ecological niche model to predict the risk areas in non-evaluated locations in Vietnam.
| 2.3.5.1 Develop protocols for integrating handheld GPS receivers into hospital and field specimen collection. GPS technology allows researchers in the field to collect precise longitude and latitude coordinates, enabling them to more precisely record the location of sample collection, as well as the scheme used to generate a representative sample. |
| 2.3.5.2 From GPS coordinates collected at hospital and field sites develop a data sheet that can be used with GIS and ecological niche modeling software. |
| 2.3.5.3 Develop protocols, standardizing data entry & formatting for use with GIS. |
| 2.3.5.4 Improve capacity to produce high-quality analysis and graphics for reports and scientific publications. |
| 2.3.5.5 Determine the potential predictive value of various geospatial and ecological niche modeling applications for characterizing spatial and temporal dynamics of C. burnetii, Rickettsia spp. and O. tsutsugamushi in Vietnam. |
1. Deliverables:
| 2.4.1 |
| DELIVERABLE (Summary) |
| DUE |
| 2.4.1.1 |
| Draft reports and develop presentation(s) for scientific/medical meeting(s) and a manuscript(s) for publication. All data shall be submitted to Principal Investigator Dr. Allen Richards. |
| Quarterly |
| 2.4.1.2 |
| Provide testing results from serological and molecular assays on human, animal, and arthropod specimens. |
| Quarterly |
| 2.4.1.3 |
| Describe prevalence and distribution of rickettsial agents in Vietnam. |
| Quarterly |
| 2.4.1.4 |
| Provide distribution maps and Ecological Niche Models, as well as, determine potential risk areas of Rickettsial disease in Vietnam. |
| Final |
| 2.4.1.5 |
| The ability to receive/use all samples collected and data generated during the course of the project for at least 12 months after the project end date. |
| Final |
| 2.4.2 |
| DELIVERABLE (Year 3) |
| DUE |
| 2.4.2.1 |
| Provide updated work plan with approved IRB protocol and SOPs, and IACUC approved/exemption protocols as needed. |
By start of work/first month.
| 2.4.2.2 |
| Collect and analyze community-based samples: perform and conduct data analysis of rickettsial, orientia and Coxiella serologic and molecular assays on human, animal and arthropod samples. |
| Collection data and associated analysis data will be reported on each enrollee at months 3, 6, 9 and 12. |
| 2.4.2.3 |
| Provide distribution maps and Ecological Niche Models, as well as, determine potential risk areas of Rickettsial disease in Vietnam. |
| Distribution map(s) will be generated from tested samples by month 12; |
| 2.4.2.4 |
| Provide technical and progress status reports of ongoing treatment study and any abstracts and/or manuscripts written for submission to scientific meetings or peer reviewed scientific journals. |
| Quarterly and final. |
| 2.4.3 |
| DELIVERABLE (Year 4) |
| DUE |
| 2.4.3.1 |
| Provide updated work plan with approved IRB protocol and SOPs, and IACUC approved/exemption protocols as needed. |
By start of work/first month.
| 2.4.3.2 |
| Collect and analyze community-based samples: perform and conduct data analysis of rickettsial, orientia and Coxiella serologic and molecular assays on human, animal and arthropod samples. |
| Collection data and associated analysis data will be reported on each enrollee at months 3, 6, 9 and 12. |
| 2.4.3.3 |
| Provide final testing results from serological and molecular assays on human, animal, and arthropod specimens. |
| By month 12. |
| 2.4.3.4 |
| Describe prevalence and distribution of Rickettsial agents in Vietnam. |
| By month 12. |
| 2.4.3.5 |
| Provide final distribution maps and Ecological Niche Models, as well as, determine the risk areas of Rickettsial disease in Vietnam. |
| Distribution map(s) will be generated from tested samples by month 12. |
| 2.4.3.6 |
| Provide technical and progress status reports of ongoing treatment study and any abstracts and/or manuscripts written for submission to scientific meetings or peer reviewed scientific journals. |
| Quarterly and final. |
Section E - Inspection and Acceptance
COR
For the purpose of this clause, the Contracting Officer’s Representative (COR) is the duly authorized representative of the Contracting Officer. The COR for this contract will be appointed at time of award.
The COR will perform inspection and acceptance of services to be provided. Inspection and acceptance will be performed at the locations listed in the contract.
COR: Dr. Allen Richards Email: allen.l.richards.civ@mail.mil
Contract Specialist: Karl Molina Phone Number: (301) 619-7223 Email: karl.o.molina.civ@mail.mil
INSPECTION AND ACCEPTANCE TERMS
Supplies/services will be inspected/accepted at:
| CLIN |
| INSPECT AT |
| INSPECT BY |
| ACCEPT AT |
| ACCEPT BY |
| 0001 |
| Destination |
| Government |
| Destination |
| Government |
| 0002 |
| Destination |
| Government |
| Destination |
| Government |
| 0003 |
| Destination |
| Government |
| Destination |
| Government |
| 1001 |
| Destination |
| Government |
| Destination |
| Government |
| 1002 |
| Destination |
| Government |
| Destination |
| Government |
| 1003 |
| Destination |
| Government |
| Destination |
| Government |
| 2001 |
| Destination |
| Government |
| Destination |
| Government |
| 2002 |
| Destination |
| Government |
| Destination |
| Government |
| 2003 |
| Destination |
| Government |
| Destination |
| Government |
| 3001 |
| Destination |
| Government |
| Destination |
| Government |
| 3002 |
| Destination |
| Government |
| Destination |
| Government |
| 3003 |
| Destination |
| Government |
| Destination |
| Government |
CLAUSES INCORPORATED BY REFERENCE
| 52.246-7 |
| Inspection Of Research And Development Fixed Price |
| AUG 1996 |
Section F - Deliveries or Performance
DELIVERY INFORMATION
| CLIN |
| DELIVERY DATE |
| QUANTITY |
| SHIP TO ADDRESS |
| DODAAC / CAGE |
| 0001 |
| POP 26-MAR-2018 TO |
25-MAR-2019
| N/A |
| NAVAL MEDICAL RESEARCH CENTER (NMRC) |
DR. ALLEN RICHARDS
503 ROBERT GRANT AVENUE
SILVER SPRING MD 20910
301-319-7668 FOB: Destination N32398
| 0002 |
| POP 26-MAR-2018 TO |
25-MAR-2019
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 0003 |
| POP 26-MAR-2018 TO |
25-MAR-2019
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 1001 |
| POP 26-MAR-2019 TO |
25-MAR-2020
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 1002 |
| POP 26-MAR-2019 TO |
25-MAR-2020
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 1003 |
| POP 26-MAR-2019 TO |
25-MAR-2020
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 2001 |
| POP 26-MAR-2020 TO |
25-MAR-2021
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 2002 |
| POP 26-MAR-2020 TO |
25-MAR-2021
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 2003 |
| POP 26-MAR-2020 TO |
25-MAR-2021
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 3001 |
| POP 26-MAR-2021 TO |
25-MAR-2022
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 3002 |
| POP 26-MAR-2021 TO |
25-MAR-2022
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 3003 |
| POP 26-MAR-2021 TO |
25-MAR-2022
| N/A |
| (SAME AS PREVIOUS LOCATION) |
N32398
| 52.242-15 |
| Stop-Work Order |
| AUG 1989 |
| 52.247-34 |
| F.O.B. Destination |
| NOV 1991 |
Section G - Contract Administration Data
| 252.204-0002 |
| Line Item Specific: Sequential ACRN Order |
| SEP 2009 |
| 252.204-7006 |
| Billing Instructions |
| OCT 2005 |
CLAUSES INCORPORATED BY FULL TEXT
252.232-7006 WIDE AREA WORKFLOW PAYMENT INSTRUCTIONS (MAY 2013)
(a) Definitions. As used in this clause--
Department of Defense Activity Address Code (DoDAAC) is a six position code that uniquely identifies a unit, activity, or organization.
Document type means the type of payment request or receiving report available for creation in Wide Area WorkFlow (WAWF).
Local processing office (LPO) is the office responsible for payment certification when payment certification is done external to the entitlement system.
(b) Electronic invoicing. The WAWF system is the method to electronically process vendor payment requests and receiving reports, as authorized by DFARS 252.232-7003, Electronic Submission of Payment Requests and Receiving Reports.
(c) WAWF access. To access WAWF, the Contractor shall--
(1) Have a designated electronic business point of contact in the System for Award Management at https://www.acquisition.gov; and
(2) Be registered to use WAWF at https://wawf.eb.mil/ following the step-by-step procedures for self-registration available at this Web site.
(d) WAWF training. The Contractor should follow the training instructions of the WAWF Web-Based Training Course and use the Practice Training Site before submitting payment requests through WAWF. Both can be accessed by selecting the “Web Based Training” link on the WAWF home page at https://wawf.eb.mil/.
(e) WAWF methods of document submission. Document submissions may be via Web entry, Electronic Data Interchange, or File Transfer Protocol.
(f) WAWF payment instructions. The Contractor must use the following information when submitting payment requests and receiving reports in WAWF for this contract/order:
(1) Document type. The Contractor shall use the following document type(s).
2 IN 1 SERVICES ONLY
(2) Inspection/acceptance location. The Contractor shall select the following inspection/acceptance location(s) in WAWF, as specified by the contracting officer.
DESTINATION/DESTINATION
(3) Document routing. The Contractor shall use the information in the Routing Data Table below only to fill in applicable fields in WAWF when creating payment requests and receiving reports in the system.
Routing Data Table* Field Name in WAWF Data to be entered in WAWF
| Pay Official DoDAAC | HQ0248 | ||
| Issue By DoDAAC | N62645 | ||
| Admin DoDAAC | N62645 | ||
| Inspect By DoDAAC | N/A | ||
| Ship To Code | N/A | ||
| Ship From Code | N/A | ||
| Mark For Code | N/A | ||
| Service Approver (DoDAAC) | N/A | ||
| Service Acceptor (DoDAAC) | N32398 | ||
| Accept at Other DoDAAC | N/A | ||
| LPO DoDAAC | N32398 | ||
| DCAA Auditor DoDAAC | N/A | ||
| Other DoDAAC(s) | N/A |
(4) Payment request and supporting documentation. The Contractor shall ensure a payment request includes appropriate contract line item and subline item descriptions of the work performed or supplies delivered, unit price/cost per unit, fee (if applicable), and all relevant back-up documentation, as defined in DFARS Appendix F, (e.g. timesheets) in support of each payment request.
(5) WAWF email notifications. The Contractor shall enter the email address identified below in the “Send Additional Email Notifications” field of WAWF once a document is submitted in the system.
allen.l.richards.civ@mail.mil
(g) WAWF point of contact. (1) The Contractor may obtain clarification regarding invoicing in WAWF from the following contracting activity's WAWF point of contact.
usn.detrick.navmedlogcomftdmd.list.nmlc-wawf@mail.mil
(2) For technical WAWF help, contact the WAWF helpdesk at 866-618-5988.
(End of clause)
Section H - Special Contract Requirements
INVENTION DISCLOSURES
INVENTIONS DISCLOSURES AND REPORTS
(a) In accordance with the requirements of the Patent Rights clause (FAR 52.227-13)of this contract, the contractor shall submit “Report of Inventions and Subcontracts” (DD Form 882) along with written disclosure of inventions to the designated Contract Administrator.
(b) The Contract Administrator will forward such reports and disclosures directly to the appropriate Patent Counsel, designated below, for review and recommendations, after which the reports will be returned to the Contract Administrator.
Address of Patent Counsel:
Office of Legal and Technology Services Naval Medical Research Center (Code 1URO) 503 Robert Grant Avenue, Suite 1W/15 Silver Spring, MD 20910
(c) The above designated Patent Counsel will represent the Procurement Contracting Officer with regard to invention reporting matters arising under this contract.
(d) A copy of each report and disclosure shall be forwarded to the Procuring Contracting Officer.
(e) The contractor shall furnish the Contracting Officer a final report within three (3) months after completion of the contracted work listing all subject inventions or certifying that there were no such inventions, and listing all subcontracts at any tier containing a patent rights clause or certifying that there were no such subcontracts.
PATIENT CARE AND MEDICAL LIABILITY INSURANCE
The character of services for health care workers that are providing patient care in clinical or administrative tasks under this contract will be categorized as non-personal services as provided for by Federal Acquisition Regulation (FAR) Subpart 37.4. Patient care will be incidental to research activities or projects supported under this contract. Alleged acts of medical malpractice by non-personal health care workers are not covered under the Federal Tort Claims Act and the contractor shall indemnify the Government against legal action alleging malpractice by such workers by way of indemnification and medical liability insurance provided by the contractor. Insurance as prescribed by FAR clause 52.237-7 shall be required for those medical personnel such as physicians or nurses providing patient care in clinical or administrative tasks consistent with standard coverage prevailing within the local community as to the specific medical specialty.
NOTICE REGARDING THE DISSEMINATION OF EXPORT-CONTROLLED TECHNICAL DATA
(a) Export of information contained herein, which includes release to foreign nationals within the United States, without first obtaining approval or license from the Department of State for items controlled by the International Traffic in Arms Regulations (ITARS), or the Department of Commerce for items controlled by the Export Administration Regulations (EAR), may constitute a violation of law.
(b) For violation of export laws, the contractor, its employees, officials or agents are subject to:
| (1) Imprisonment and/or imposition of criminal fines; and |
| (2) Suspension or debarment from future Government contracting actions. |
(c) The Government shall not be liable for any unauthorized use or release of export-controlled information, technical data or specifications in this contract.
(d) The contractor shall include the provisions or paragraphs (a) through (c) above in any subcontracts awarded under this contract.
PROTECTION OF HUMAN SUBJECTS
(a) The performance of research involving human subjects shall be conducted in accordance with Defense Federal Acquisition Regulation Supplement (DFARS) clause 252.235-7004 “Protection of Human Subjects,” 32 CFR 219 “The Common Rule,” 10 USC 980 “Limitation on Use of Humans as Experimental Subjects,” Department of Defense (DoD) Instruction 3216.02 “Protection of Human Subjects and Adherence to Ethical Standards in DoD-Supported Research,” and Secretary of the Navy Instruction 3900.39 (series) “Human Research Protection Program,” as well as other applicable federal and state law and regulations, and Department of the Navy guidance. The Contractor must be cognizant of and abide by the additional restrictions and limitations imposed on the DoD regarding research involving human subjects, specifically as they regard vulnerable populations, recruitment of military research subjects, and informed consent and surrogate consent and chemical and biological agent research. Food and Drug Administration regulation and policies may also apply. The Contractor shall rely on the local command’s designated Institutional Review Board (IRB) as the IRB of record for the research to be supported under the contract. The Contractor shall also comply with all research training requirements directed by the local command.
(b) The Contractor shall hold an active (i.e., not expired) Federalwide Assurance (FWA) appropriate for research to be supported under the contract. The FWA shall remain active for the duration of the contract. The FWA is issued by the Department of Health and Human Services.
(c) The following requirements must be completed prior to the Contractor’s performance of research involving human subjects or expenditure of funding on such effort, whichever occurs first:
(1) The Contractor shall enter into a DoD Institutional Agreement for Institutional Review Board (IRB) Review (IAIR) with the local command. The IAIR will apply to all human subject research supported under the contract. The IAIR shall be executed by the parties no later than 30 days after the effective date of the contract, or before commencement of performance of research involving human subjects or expenditure of funding, whichever occurs first.
(2) Contractor personnel providing support under the contract shall complete initial and ongoing research ethics and human subject protections training appropriate to each individual’s level of involvement, duties, and responsibilities. Specific training requirements will be provided by the COR.
(3) The Contractor shall obtain written notice from the local command that: (i) Contractor personnel identified as supporting human subject research under the contract have been added to the applicable research protocol; (ii) performance of the protocol has been approved by the Command’s Institutional Official and that performance may begin; (iii) a determination that the protocol meets exemption criteria including the exemption category or classification of research risk (e.g., minimal risk); (iv) confirmation of continuing acceptability of the Contractor’s assurances; and (v) Human Research Protection Official (HRPO) review of the protocol in accordance with DFARS clause 252.235-7004 has been completed. Contractor personnel shall not commence performance of research involving human subjects until stated notice is received.
(4) The Contractor shall notify the local command of personnel changes under the contract. New personnel that will perform research involving human subjects will be required to complete applicable training and will be added to the applicable research protocol(s) as discussed above.
(d) The Contractor shall support administrative efforts by the local command to ensure compliance with the terms of this requirement. This support includes identifying Contractor personnel that may support human subject research under the contract and maintaining records of training and other documentation to demonstrate compliance with human research protection requirements under the contract. The Contractor shall also assist with the continuing review of the human subject research that is supported under the contract.
(e) Failure of the Contractor to comply with the terms of this requirement will result in the issuance of a stop-work order under Federal Acquisition Regulation clause 52.242-15 Alt. I to immediately suspend, in whole or in part, work and further payment under this contract, or will result in other issuance of suspension of work and further payment for as long as determined necessary at the discretion of the Contracting Officer.
(f) The terms of this requirement are applicable to and shall be included in all subcontracts that may include the support of human subject research.
PROTECTION AND USE OF ANIMALS (R&D Support Services)
(a) All activities involving animal subjects shall be conducted in accordance with DoD Instruction 3216.01 “Use of Animals in DoD Programs”, Secretary of the Navy Instruction (SECNAVINST) 3900.38 (Series) “The Care and Use of Laboratory Animals in DOD Programs”, 9 CFR (parts 1- 4) “Animal Welfare Regulations”, National Academy of Sciences Publication “Guide for the Care & Use of Laboratory Animals”, as amended, and the Department of Agriculture rules implementing the Animal Welfare Act as amended (7 U.S.C. 2131-2159), as amended, as well as other applicable federal and state law and regulation and DoD guidance. The contractor shall also comply with all training requirements directed by the Command's Institutional Animal Care and Use Committee (IACUC) and associated department of the Navy policies and procedures.
(b) Research under this contract involving the use of animals is based upon required institutional approvals being obtained by the Department of the Navy. Deviation from the approved research involving the use of animals is not allowed.
(c) The Department of the Navy reserves the right to conduct a post award site visit to any contractor or subcontractor facility where animal work will take place.
(d) Non-compliance with any provision of this term and condition or with the incorporated regulations and policy, will result in the issuance of a stop-work request to immediately suspend, in whole or in part, work and further payment under this contract, or will result in other issuance of suspension of work and further payment for as long as determined necessary at the discretion of the Contracting Officer.
PRIVACY ACT AND HIPAA
The contractor shall ensure that all Protected Health Information (PHI) is protected in accordance with the Privacy Act of 1974 and the Health Insurance Portability and Accountability Act of 1996 (HIPAA) mandated safeguards to ensure confidentiality of health information. All contractor personnel are required to complete HIPAA training within one (1) year prior to the provision of services under this contract. Contractor personnel must complete HIPAA refresher training annually.
ENVIRONMENTAL STANDARDS
Note: This requirement applies to work performed at the contractor’s or subcontractor’s facility.
By accepting funds under this contract, the contractor assures that it will:
Comply with all applicable standards, orders, or regulations issued pursuant to the Clean Air Act (42 U.S.C. 7401, et seq.) and Federal Water Pollution Control Act (33 U.S.C. 1251, et.seq.), as implemented by Executive Order 11738 [3 CFR, 1971-1975 comp., p. 799] and Environmental Protection Agency (EPA) rules at 40 CFR Part 15.
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