Strengthening Laboratory Capacity to Improve the Availability and Accuracy of COVID-19 Diagnosis in Peru

  • Contractor
  • , Peru
  • TBD USD / Year
  • Abt Associates profile




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Abt Associates

PLEASE view full RFP here: bit.ly/3qWhdOa

bit.ly/3qWhdOa

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Background**

The Local Health System Sustainability Project (LHSS) helps low- and middle-income countries transition to sustainable, self-financing health systems as a means to support universal health coverage. The project works with partner countries and local stakeholders to reduce financial barriers to care and treatment, ensure equitable access to essential health services for all people, and improve the quality of health services.

Peru has been one of the most affected countries in Latin America by the COVID-19 pandemic. The national response to COVID-19 has been complicated by a fragmented health sector, with poorly responsive primary health care and very limited capacity for intensive care. In addition, the high level of informal labor has prevented many people from adhering to government-imposed preventive measures, leading to continued transmission.

One of the key aspects of the response to the pandemic is diagnostic capacity and laboratory surveillance. In Peru, during the first months of the pandemic, the diagnosis of COVID-19 was only made through molecular tests at the National Institute of Health (NIH), which is in charge of leading the network of public health laboratories. Gradually this capacity was expanded and by 2022 there are 124 laboratories that have been authorized to carry out molecular tests, all of them located in Lima, capital of the country, and in the capitals of the departments. Of these, 5 belong to the National Institute of Health (NIH); another 52 are located in the Regional Health Directorates, public hospitals and EsSalud1 hospitals; 6 belong to universities; and 61 are private laboratories. Samples for molecular tests are taken in health facilities throughout the country, from which they are transported to authorized laboratories. The proliferation of cases has led to an immediate need to increase sample collection and test processing at national and regional public health laboratories. Although a careful evaluation of the quality of the sampling and the conditions of transport has not been carried out, it is known that there are deficiencies in the taking of samples, inadequate biosecurity, disruption of the cold chain, among other problems that could affect the diagnosis.

1 EsSalud: Social Health Insurance.

In addition, quality control of polymerase chain reaction (PCR) tests has not yet been implemented in regional public health laboratories and testing capacity in university laboratories has not yet been utilized.

Between the notification of the first case of COVID-19 in Peru in March 2020 and the first week of February 2022, samples from 26 million people have been analyzed and 3.4 million cases have been diagnosed, of which 1 million have been diagnosed by PCR2 and 15 thousand genomes have been sequenced3. Only 380 genetic sequencings are carried out weekly in the NIH laboratories, plus a smaller number in the laboratory of a private university in Lima. The European Commission has urged countries to increase the rate of genomic sequencing to identify the progression of variants or detect new ones. Member States were asked to sequence at least 5%, and preferably 10%, of positive COVID-19 test results, minimize delays in results and ensure that this data is shared, so that comparisons can be made4. In Peru, during the last weeks the average number of positive tests is 20,000 per week, so following the recommendations of the EC, it would be necessary to carry out at least 1,000 sequencings per week. As can be seen, the genomic sequencing capacity is limited.

In this context, LHSS will provide technical support to national laboratories and in selected regions to strengthen and ensure equitable access to COVID-19 diagnostic capacity. LHSS held initial discussions with the National Institute of Health to identify priority needs to improve testing and processing of COVID-19 samples, focusing on increasing diagnostic accuracy and results turnaround time. Therefore, technical cooperation will be aimed to achieving improvements in three aspects: collection and transport of samples; PCR quality control; and scale-up of genomic sequencing.

Objective

The general objective of this award is to strengthen laboratory capacity to improve PCR test availability and accuracy, and to make progress towards increased capacity for genomic sequencing. To achieve this general objective, the following specific objectives must be achieved:

• Improve the sample collection process, biosafety conditions and transport of PCR samples to certified laboratories,

• Ensure the reliability of COVID-19 PCR testing results.

• Develop a proposal for the expansion of genomic sequencing with technologies appropriate to the reality of Peru.

Approach

To accomplish this, LHSS will engage a subcontractor to develop the following activities:

  1. Sample Collection and Transport Process

Conduct a rapid assessment of the sample collection process, biosafety conditions and transport of samples to reference laboratories ensuring the cold chain in designated COVID-19 testing locations

2 Health Situation Room COVID-19. Summary of the country’s current situation. National Center for Epidemiology, Prevention and Disease Control. Ministry of Health of Peru.

3 NIH. Genomic sequencing of the SARS-CoV-2 virus in Peru.

4 European Commission. Communication from the Commission to the European Parliament, the European council and the council. A united front to beat COVID-19. [Internet]. 2021 [citado 13 de julio de 2021]. Available in: https://ec.europa.eu/transparency/documents-register/detail?ref=COM(2021)35&lang=en

in Lima and two regions, selected in coordination with the NIH and LHSS, to identify challenges and gaps in key areas (HRH, processes, equipment and facilities). Thus, this pre-analytic component must look at aspects such as available specimen collection platforms; human resource capacity and training needs for SARS-CoV-2 related IPC; and safe specimen collection, handling, packaging, storage, and transport.

Based on the findings from the rapid assessment, and in coordination with the NIH, the subcontractor will develop a training plan for laboratory staff. The plan must include standard operating procedures for COVID-19 sample analysis, handling, and transportation to reference laboratories and recommendations to meet laboratory capacity needs in pandemic and non-pandemic contexts. The subcontractor will use the training plan to provide training for laboratory staff, selected with the National Institute of Health. The training will be focused on improving laboratory practices for COVID-19, based on the needs identified in the rapid assessment.

  1. PCR Testing

Conduct a rapid assessment to evaluate PCR testing procedures in selected laboratories to evaluate the quality of results and ensure quality assurance and control processes are followed. The assessment will focus on the analytic and post-analytic phases of SARS-CoV-2 case detection with an emphasis on IPC; equipment and consumables; human resources; and information technology needs at each phase.

• Thus, the analytic component will look at equipment and consumables needs for PCR or other approved testing platforms; actual and potential daily SARS-CoV-2 processing capacity across different platforms and sectors; diagnostic efficiencies (this includes the cost effectiveness of different tests, GeneXpert versus standard PCR testing taking into account the cost per test, staff, management and turn-around time); human resource capacity and training needs for specimen processing and Biosafety level 2 (BSL2 ); IT capacity and needs for case detection; routine and surge lab capacity requirements if all tests and results should be turned around within 24 hours; lab supply chain and management systems for consumables.

• The post-analytic component will look at quality assurance mechanisms and the role of the NIH in supervision and capacity building for quality improvement (QI); quality assurance mechanisms and levels of accreditation, connection of the laboratory network in terms of operations and communication; and data recording, reporting and data management between COVID-19 identified laboratories and reporting lines to the NIH.

Based on findings from the evaluation, the subcontractor will develop a systematized process, including the development of a detailed checklist, for external performance evaluation of COVID-19 PCR testing in laboratories to ensure the reliability of the results. The subcontractor will train laboratory staff in charge of supervising quality of results to implement the external performance evaluation checklist and reinforce quality assurance and control protocols. The possibility of incorporating the external performance evaluation into the existing National Institute of Health’s licensing process for laboratories must be discussed.

  1. Genomic Sequencing

Conduct a rapid assessment of genomic sequencing capacity at the national level and develop a proposal for its expansion, including identification of context-appropriate technologies, existing

capacity and training needs of sub-national laboratory personnel, and the possibility of leveraging other existing resources in the country.

The subcontractor will define the methodology of the assessments, including determining the appropriate samples of points of specimen collection and laboratories. All the assessments will be grounded in standardized technical guidelines, regulatory checklists and laboratory assessment tools used by WHO, US CDC and other best practice technical guidance.

To support these activities, the LHSS and the NIH will form a “Support Committee” to accompany and monitor the progress of the activities, as well as to facilitate the subcontractor’s access to the laboratories and their interaction with relevant actors and organizations.

Expected tasks

The subcontractor is expected to carry-out the following tasks:

I. Develop the work plan, including specific objectives, methodology, activities, and work schedule.

II.Prepare for the assessments

a. Review the approaches and international guidelines about COVID-19 molecular diagnosis and genomic sequencing.

b. For each one of the three group of activities:

Define the methodology for selecting the sample according to its relevance to the objectives of the assessment.

Define the information to be collected (regulatory, administrative, organizational, of processes) and the procedures for gathering this information.

Develop an assessment tool based on international best practices and standards, and NIH tools and guidelines.

Define the procedures for the collection of information in Lima, Ayacucho y Huanuco.

Define the data collection instruments to be used during the study.

Define an analyzing plan for the information collected.

c. Present and discuss the proposal of workplan with the Support Committee and reach agreement on the plan before moving forward.

III. Data collection for each assessment

a. Conduct a desk review of processes, policies, quality tools, and existing reports.

b. Conduct site visits and collect data as defined in the proposed methodology.

c. Conduct interviews with stakeholders defined in coordination with the support committee.

IV. Analysis and presentation of assessments findings

a. Analyze the collected information and elaborate the results obtained for each group of activities in accordance with the objectives set.

b. Produce a draft assessment report for review by the Support Committee.

c. Present and discuss the findings with the LHSS and NIH teams.

d. Prepare a report of findings which must incorporate and address the comments received

from the LHSS and NIH teams.

V. Develop of improvement proposals

a. For the Sampling and Transport Process:

Prepare a Training Plan and training materials for the staff of the labs and points of specimen collection.

Define with the NIH team the list of personnel who will be trained.

Implement the Training Plan.

b. For the PCR testing:

Elaborate a systematized process, including the development of a detailed checklist for external performance evaluation of COVID-19 PCR testing in laboratories to ensure the reliability of the results.

Discuss with the NIH team the possibility of incorporating external performance evaluation as part of the authorization/supervision processes that the NIH applies to laboratories that perform or want to perform PCR.

Develop training materials and provide training to laboratory staff in charge of supervising quality of results to implement the external performance evaluation checklist and reinforce quality assurance and control protocols.

c. For the Genomic Sequencing:

Prepare a proposal for the expansion of genomic sequencing including identification of context-appropriate technologies, existing capacity and training needs of sub-national laboratory personnel.

Present and discuss the proposal of workplan with LHSS and NIH teams.

VI. Preparation of the final report.

Prepare the final report of the intervention implemented to strengthen the capacity of the laboratory to improve the availability and accuracy of the tests and the genomic sequencing, detailing the work carried out for each group of activities.

Expected deliverables

Deliverables

Due Date

Report 1: Work Plan with specific sections for each

May 16, 2022

group of activities. For each section the plan must

include at a minimum the specific objectives,

methodology, activities, and a work schedule by weeks.

Report 2: Assessment findings. This report must include:

June 27, 2022

2.1. Assessment finding of Sampling and Transport

Process. The report must include a methodology

section with details about selecting sample,

instruments, procedures and assessment tools used.

The finding section must incorporate and address the

comments received from the LHSS and NIH teams.

2.2. Assessment findings of PCR Test. The report must

include a methodology section with details about

selecting sample, instruments, procedures and

assessment tools used. The finding section must

incorporate and address the comments received from

the LHSS and NIH teams.

2.3. Assessment findings Genomic Sequencing. The

report must include a methodology section with

details about instruments, procedures and assessment

tools used. The finding section must incorporate and

address the comments received from the LHSS and

NIH teams.

Report 3: Proposal of Training plan to improve Sampling

July 11, 2022

and Transport Process.

Report 4: Recommendations and proposal of

July 18 2022

Systematized process for external performance evaluation

of COVID-19 PCR testing in laboratories to ensure the

reliability of the results. This report must include the

checklist and any other tools developed.

Report 5: Recommendations and proposal for the

July 25, 2022

improvement and expansion of genomic sequencing

including identification of context-appropriate

technologies, existing capacity and training needs of sub-

national laboratory personnel.

Report 6: Report of the training implementation for

August 15, 2022

improve Sampling and Transport Process and for the

PCR external performance evaluation, including training

materials.

LHSS Short-Term Technical Assistance Report (format

August 31, 2022

to be provided to consultant)

Budget:

• Estimated funding available for this activity is from $320,000 to $375,000 (including taxes).

Organizational Qualifications:

  1. Expertise in biological sciences or medical technology and research.

  2. At least seven years of organizational experience in safety and quality in diagnostic testing and laboratories.

  3. Specific experience in molecular diagnostic testing (all phases) and genomic sequencing for SARS-CoV-2.

  4. A College of American Pathologists Certification (CAP) or equivalent accreditation and accredited lab inspectors for medical labs.

  5. Experience in developing training materials and delivering training.

  6. Experience in strengthening lab capacity.

  7. Experience working with the Ministry of Health or National Public Health Laboratories or equivalent in Peru or other countries.

[End of Section 1]**

SECTION 2 – INSTRUCTIONS TO OFFEROR

1. POINT OF CONTACT

Proposal should be submitted electronically via email to no later than 8:00 pm (ET) on April 15, 2022, to: [email protected] with a copy to [email protected].

2. QUESTIONS

Questions must be submitted in writing to: Edgardo Nepo at [email protected] by 2.00 p.m. (ET) on April 8, 2022.

To ensure the integrity of the proposal process, communications with anyone other than the issuer of this solicitation will not be considered in the award decision and may be grounds for rejection of your proposal.

Questions must be submitted in writing by the date and time stated above to allow sufficient time to provide all solicitants a response. Questions received after that time may not be answered prior to the proposal due date.

If any discrepancy, omission, or ambiguous information is found in this proposal package, please notify the issuer of the solicitation and cite the specific section in question.

Answers to any inquiry will be communicated simultaneously to all prospective solicitants if the information provide within is necessary to submit a proposal, or the lack thereof would be prejudicial to other solicitants, ensuring the consistency of the proposal process. The source of the inquiry will not be disclosed.

3. RESPONSIVE PROPOSALS

Solicitants must examine all instructions, forms, terms, and specifications in the proposal documents and submit proposals in accordance with those provisions. Failure to submit all required information or submission of a proposal not responsive to the proposal documents may result in the rejection of the proposal.

That being said, solicitants are invited to be innovative in their proposals. Meeting or exceeding

Abt’s stated objectives with less expenditure or in a shorter timeframe will be looked upon favorably. Any alternative solutions should be clearly noted and detailed in the technical proposal section of your response.

4. CURRENCY

All proposals must be stated in U.S. Dollars. Abt intends to award the subcontract in U.S. Dollars, with payments denominated in U.S. Dollars unless there are conditions or restrictions that require the subcontract value and/or payments be made in local currency.

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RFP# X_2022

5. PAYMENT TERMS

Abt requests solicitants to offer their best payment terms. Payment terms will be taken into consideration during the proposal evaluation process.

6. DOCUMENTS REQUIRED WITH PROPOSAL:**

7. 1. Representations, Certifications, and Other Statements of Offerors Form PROPOSAL FORMAT

A. General Preparation of Proposal:

a. Offerors are expected to review, understand, and comply with all aspects of this RFP.

b. Each offer shall furnish the information required by this RFP. Technical & financial proposal signed by an agent shall be accompanied by evidence of that agent’s authority, unless that evidence has been previously furnished to the issuing office.

c. Offerors should retain for their records one copy of the proposal and all enclosures which accompany it.

d. Proposal shall be split into two separate parts: (1) Technical; and (2) Cost. The formats for each of these parts of the proposal are set forth below.

B. Technical Proposal Format

The Technical Proposal will be submitted in English language, typed, on company letterhead, single-spaced, with each page numbered consecutively (maximum 20 pages total, excluding the annexes). The technical proposal should be specific, complete and presented concisely. Proposal should demonstrate the organization’s capabilities and expertise with respect to achieving the goals of this program. Offers are invited to present the following sections:

a. Cover Page

  1. State that the technical proposal is made to the LHSS and Abt Associates Inc.

  2. Provide the full legal name, address, telephone and fax number of the organization submitting the proposal, and the date of submission.

b. Technical Approach

This section should include a narrative or outline presentation describing how the Scope of Work will be accomplished – as well as a suggested plan for carrying out the Scope of Work (SOW). The offeror must also include a timeline showing the dates when activity milestones will be met and deliverables will be submitted to Abt Associates for approval.

c. Management plan (not to exceed 3 pages, excluding resumes)

The offer should propose a management plan and describe how the proposed plan will contribute towards achieving the objectives and results described in the statement of work Section 1. The proposed plan should specifically state and justify the composition and organizational structure of the entire project team. It

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should also describe how the technical expertise and experience of all staff members is most conducive to achieving expected results of the Family planning social and behavior change campaign.

The plan should specify the role and estimated amount of time each staff member will devote to the project and/or specific components within the project. The management plan should also describe how the organization would coordinate its activities with the LHSS. CVs for the staff assigned to the project shall be attached as an Annex to the proposal.

d. Firm Experience and Past Performance (2 pages):

The Offeror should provide corporate capabilities and past performance statement that include the following components:

a. A background summary outlining the Offeror’s expertise.

b. A description of specific experience that is relevant to the statement of work.

c. A current list (within the past 5 years) of relevant clients with references that can be contacted (please provide names and current phone numbers or email addresses). The list should include at least two references from completed projects that can attest to the Offeror’s competency in conducting similar qualitative research assignments.

C. Cost or Business Proposal Format

Instructions for Preparation of the Cost or Business Proposal

The Cost or Business Proposal is to be submitted under separate cover from the technical proposal. Certain documents are required to be submitted in order for Abt Associates to make a determination of responsibility. There is no page limitation on the Cost or Business Proposal.

A detailed budget with an accompanying budget narrative that provides in detail the rationale for proposed costs. The budget narrative should provide information regarding the basis of estimate for each line item, including reference to sources used to substantiate the cost estimate (e.g. organization’s policy, payroll document, vendor quotes, etc.). The Offeror must propose costs that it believes are realistic and reasonable for the work in accordance with the Offeror’s technical approach.

The Cost or Business Proposal shall also include a statement indicating that the proposal remains available for acceptance by Abt Associates for a minimum of ninety (90) calendar days after the closing date of this RFP. The transmittal letter must include a summary of the proposal and its total cost and be signed by an individual authorized to commit the organization. As part of the Cost or Business Proposal (Attachment 2) and shall include:

Budget Breakdown

Break down proposed costs in sufficient detail in the attached budget template to permit cost analysis. The budget shall be denominated in local currency only.

Cost estimates must be submitted in Excel format using the attached budget template. The file must be unprotected and there should be no hidden columns/rows/cells. Each cost element must include a basis for estimate or rationale. Any budget submitted without explanatory notes or in a different template will not be accepted and the proposal will not be considered.

The budget template contains a budget tab explaining each category

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SECTION 3 TERMS AND CONDITIONS

  1. The following terms and conditions, supplements, representations and certifications are applicable and will be incorporated in any subcontract awarded as a result of this solicitation:

• Prime Contract Flowdowns (Attachment 2)

  1. Incurring of Costs

This solicitation does not commit Abt to pay any costs incurred in the submission of any proposal, or incurred in making necessary studies or designs for the preparation thereof, or to acquire or contract for any service.

  1. Proprietary Information

Offerors must identify any drawings, and or data, that are of a proprietary nature contained within their proposal. Abt will not receive or provide any proprietary information without an executed Proprietary Information Agreement. Abt assumes no obligation of confidentiality for anything transmitted in a proposal package that is not properly identified.

  1. Rights of Abt

Abt reserves the right to:

• Amend by addenda any part of this solicitation;

• Reject any or all offers received in response to this solicitation;

• Waive informalities or minor irregularities in offers received;

• Enter into discussions, clarifications, or negotiations with offerors on any or all aspects of their proposal;

• Accept any proposal in whole or in part without prior negotiations;

• Cancel and/or reissue this solicitation;

• Award one or more contracts to one or more offerors; and

• Retain all proposals submitted in response to this solicitation as the property of Abt.

  1. False Statements

Offerors must provide full, accurate, and complete information as required by this solicitation and the documents incorporated herein. The penalty for making false statements in proposals is prescribed in 18 U.S.C. 1001, and applicable to all federal contracts.

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SECTION 5 – EVALUATION AND REVIEW INFORMATION

1. EVALUATION CRITERIA

Proposals received in response to this RFP will be evaluated using the evaluation criteria set forth in this Part.

The criteria presented below have been tailored to the requirements of this RFP that Offeror should address in their proposal, and to set standards against which the proposal will be evaluated. Proposals will be evaluated in accordance with the evaluation criteria set forth below:

Technical Proposal

• Technical Approach overall responsiveness and understanding to the Statement of Work (40 points)

• Past Performance Experience in laboratory sciences, quality testing standards and best practices (30 points)

• Team CVs including lead CAP certified inspector and other data collection and analysis team members (30 points)

Evaluation Criteria

Sub-

Total

criteria

Points

Points

1. Firm Past Performance Experience and team espertise

60

1a

Past Performance Experience in laboratory sciences, quality testing

30

standards and best practices

1b

Team expertise, evaluated by the CVs of the team leader (CAP certified

30

or equivalent) and key team members.

2. Technical Approach and Methodology

40

2a

Technical Approach overall responsiveness and understanding to the

40

Statement of Work, including feasibility and reflecting a strong technical

approach to implementation

Total Technical Proposal

100

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Cost Proposal

Cost Proposal evaluation will be based upon the cost proposal and the supporting narrative provided by the offeror. Cost proposal will be evaluated but will not be assigned a score. The evaluation of cost will include a determination of cost realism, completeness, and reasonableness. See Attachment 1 – Cost Application (Budget notes and Budget Template)

o (1) An analysis of the proposed cost will be conducted to determine the validity and the extent to which it reflects performance addressed in the technical proposal.

o (2) Cost/price evaluation will be performed to determine whether the proposed cost/prices are realistic for the work to be performed, reflect a clear understanding of the requirements, and is consistent with the unique methods of performance set forth in the offeror’s technical proposal and budget narrative.

o (3) A cost realism analysis may be performed to determine whether the proposed costs and level of effort are realistic for the work to be performed under the RFP, reflects a clear understanding of the requirements, and is consistent with the unique methods of performance set forth in the offeror’s technical proposal and budget narrative. This evaluation is conducted with the expectation of adequate cost/price competition and will rely heavily on market forces to determine whether the proposed cost/price is fair and reasonable. The comparison of proposed cost/price in response to this solicitation is the preferred technique for this evaluation. Abt may also compare the proposed cost/price to historical cost/price paid for the same or similar services or independent estimates. Other techniques and procedures if deemed necessary, may be used to ensure proposed cost/price is fair and reasonable.

  1. SELECTION

Abt intends to make the award without discussion however if discussion is necessary Abt may establish a competitive range composed of the most highly rated proposals and request final offers.

Abt intends to select a winning offer based on the criteria listed above. Abt Associates will determine the overall proposal score by using the tradeoff method to select the best value offer taking into consideration the evaluation for the technical and cost proposals. The cost proposal will be evaluated separately


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