Innovations in Low-Cost and Simplified Pathogen Sequencing Workflows

Eligibility

Who is eligible for grants?
This opportunity is open to research institutes, nonprofit organizations, for-profit companies, international organizations, government agencies, and academic institutions. Please note that all applicants will be expected to comply with the Gates Foundation's global access requirements. We encourage projects and/or consortia applications led by applicants from Low- and Middle-Income Countries (LMICs). Individuals and organizations classified as individuals for U.S. tax purposes are not eligible to receive an award under this RFP.

Eligible entities must not be subject to United Nations sanctions or have committed serious violations of United States or UN sanctions. Eligible entities must not have derived revenue from the production of controversial weapons (such as antipersonnel landmines, cluster bombs, or nuclear bombs) or the production or manufacture of tobacco.

Upon registration, applicants must provide information about the tax status of their organization as different terms and conditions may apply. You should confirm your organization's tax status with the appropriate advisor or entity within your organization such as your grants or contracts department, finance, or office of sponsored research.

Can individuals or unaffiliated teams apply directly?
No. Individuals and organizations classified as individuals for US tax purposes are not eligible to receive an award. A newly formed team without an eligible legal entity would need to apply through, or partner with, a qualifying organization.

Are applicants from outside the US eligible, and are LMIC-led applications encouraged?
Yes to both. There is no country restriction beyond the sanctions and eligibility rules, and projects/consortia led by LMIC applicants are highly encouraged.

Is a partner mandatory?
Partnerships and multidisciplinary consortia are encouraged (successful projects often need expertise spanning laboratory science, public health, bioinformatics, implementation, and product development), but partnerships are not required. The Foundation is unable to facilitate partner matching during the application period, though collaboration opportunities may arise later in the selection process.

Is there an LMIC co-lead requirement or a minimum LMIC budget share?
No, there is no required LMIC co-lead and no minimum budget allocation for LMIC partners. However, reviewers will consider how accessible, practical, and sustainable the proposed approach is in LMIC settings, and strong plans for equitable access, adoption, and implementation are encouraged.

Can PhD fellows or students apply?
There are no specific degree requirements, but the Primary Investigator (PI) must demonstrate the relevant expertise, experience, and organizational support needed to successfully lead the project.

Can any industry or manufacturing company be a partner?
Yes; as long as they meet the eligibility criteria.

Would a proposal led by an African national public health institution, with technology and scientific partners from Asia and Europe, be viewed as fully aligned with the intended regional collaboration model? Is cross-validation in both an African and an Asian LMIC expected or preferred?
This RFP is open to applicants from LMICs. Partnership is encouraged given the complexity and ambition of the goal, but LMIC-led proposals will be encouraged rather than prioritized simply for being LMIC-led - prioritization depends on cost, simplification, and innovation rather than geographic origin. No specific partnership structure is required.

Can a participant from a LMIC with primary affiliation in a non-LMIC-based lab be eligible?
Yes - applicants from non-LMIC countries are eligible and encouraged.

Can a proposal be submitted representing a country, or can only organizations apply?
Only registered organizations are eligible. Government agencies are eligible.

Is it a must for the partnership to be from different countries?
No, this is not required.

Does the age of the applicant organization (for-profit company) matter?
No, as long as they meet the eligibility criteria in the RFP.

Are current Gates funding awardees eligible for this opportunity?
Yes.

Can commercial manufacturers or technology developers be included as consortium partners? If yes, are there any restrictions on their role or funding?
Yes, they are eligible to be included as consortium partners and there aren't any restrictions other than what is outlined in the eligibility criteria. 

Does a public health department in the USA qualify to apply?
Yes. 

Application Process

What must my application include?
Please refer to the Application Instructions document.

Am I able to edit my proposal once submitted?
Yes, you may edit your proposal up until the specified deadline.

What amount of indirect cost is available?
Details of the foundation's indirect cost policy guidelines can be found here: Gates Foundation's indirect cost policy. 

Can organizations apply multiple times or submit multiple ideas?
A given PI can be the lead/main applicant on only one application, but individuals can be collaborators on multiple applications. So an organization can apply multiple times, as long as each application has a different lead PI.

Scope

What costs count towards the $10 target and how is it measured?
The target is the total per-sample cost from sample to sequence. It's measured by what the applicant submits as proof - an estimate of the cost of each component of the assay - so reviewers can assess whether the proposal falls within the $10 target.

Must the $1-10 target already be achieved at the time of application?
No. The RFP is meant to encourage and support innovations that can lead toward the $10 target, even if that target isn't reached yet. Early-stage ideas are eligible.

Can proposals optimize existing platforms and workflows?
Yes, this is highly encouraged. However, compatibility with existing instruments (e.g., Illumina, Oxford, MGI, and others) is required.

Can a proposal address only one segment of the workflow rather than the full pipeline?
Yes, as long as the change to that specific segment helps achieve the $1-10 cost target.

Are non-sequencing (e.g., PCR-based) assays eligible?
No. This RFP focuses only on sequencing-based assays; proposals that do not involve a sequencing-based assay are out of scope.

How does the platform-agnostic preference affect technology-specific proposals?
Platform agnosticism and multi-platform compatibility are desirable and preferred, but not mandatory.

What does the exclusion of "increased multiplexing and throughput" mean?
The RFP is not looking for cost reduction achieved simply by increasing throughput - it's a well-known fact that cost drops as throughput rises, but throughput is often not available in LMIC settings. The focus is on assay-level cost reduction, not throughput-level cost reduction.

Are targeted amplicon or metagenomic approaches both in scope?
Yes. Any sequencing-based methodology (amplicon, targeted with or without enrichment, metagenomic, etc.) is eligible as long as it relates to the listed use cases and reduces cost and complexity.

Are hybrid approaches that combine targeted and untargeted sequencing eligible?
Yes - this could represent a new form of innovation.

Is the pathogen list in Table 1 exhaustive?
No, it is an illustrative/priority list. The viral category, for example, is described as "public health relevant viruses," which is broader. Any pathogen of public health priority could be eligible, though priority will be given to the pathogens listed in the RFP document.

Must extension to additional pathogens be demonstrated with data?
No. A roadmap for adaptability is sufficient - applicants do not need to demonstrate adaptability with data, but they should clearly outline the roadmap.

What technical maturity is expected?
All maturity levels are eligible, from early-stage ideas and proof-of-concept work (Tier 1) through more mature methodologies (Tier 3), as long as there's a clear pathway toward lowering cost and simplifying the assay.

What quality, turnaround, and data governance standards apply?
Data quality must meet the minimum standard needed to support public health decision-making. Turnaround time should be reasonable but depends on the pathogen and use case (e.g., outbreak detection needs faster turnaround than surveillance of an endemic pathogen). All applicants must comply with the Gates Foundation Global Access requirements.

Can the proposal include analytical development to reduce turnaround time from sample to decision-making, not just data?
The turnaround time indicators are for sample-to-data, not sample-to-decision, since decision-making depends on several other factors. The scope is limited to data generation.

What is the intended care setting (local clinic, district, regional lab, national center), and what throughput should be assumed for cost estimates?
The cost estimate is independent of throughput - it's a cost-per-assay estimate. The estimation is based on national-level reference labs (using an African setting as an example), not clinic-level or subnational-level settings.

Does the $1–10 per-sample target apply to the entire workflow (DNA extraction, amplification, library preparation, sequencing), or only the sequencing component?
It applies to all of it - from sample to sequence, including extraction, library preparation, and sequencing.

Could you provide more specific criteria regarding cold chain requirements?
Cold chain independence is not a mandatory requirement - it is preferred. For example, lyophilized assays would be a good example of meeting this preference, given supply chain challenges, but it is not required.

What is the average cost at the moment, and what is the rationale behind the $10 target - what exactly does it cover?
The $10 target came from several cost assessments conducted across different geographies and emerging markets. The team recognizes it is ambitious, but feasible, and hopes to reduce cost together with applicants through innovation. The target covers sample to sequence (extraction may or may not be included, since some approaches could be extraction-free) but does not include bioinformatics analysis - a FASTQ-like file would be sufficient output for this RFP. Achieving $10 exactly is not required; any credible pathway that gets closer to that target is eligible.

What level of multiplexing would be considered reasonable?
This is highly use-case specific. Cost reduction achieved solely through multiplexing/increased throughput is not eligible - there must be an innovation component to the workflow. Increasing throughput together with other innovations could be considered, but a general multiplexing target is difficult to specify given the variety of use cases in the RFP.

Since sequencing cost per sample is split across samples in a sequencing run, we need to assume a throughput to estimate per-sample cost. Is there a good base number to use?
There's no fixed throughput target - it's very difficult to set one given the range of pathogens and use cases (e.g., small viral pathogens vs. bacteria vs. malaria). Applicants should submit their proposal at whatever throughput allows them to achieve the target cost, and reviewers will assess it. Inclusion of this information is desirable.

Can we talk about cost per usable genome?
Yes, that's acceptable - "usable" in this context meaning a good-quality genome.

What is the rationale for bulk procurement price negotiation being out of scope, given that these are part of the routine supply chain optimizations countries need to pursue?
The Gates Foundation is addressing supply chain-related challenges (including bulk procurement and price negotiation) separately, through other partnerships and a separate RFP. This RFP is focused only on innovation at the workflow/sequencing level, from sample to sequence.

Does multiplex PCR using specific primers to amplify selected genes, and LAMP-based assays, qualify as targeted/amplicon sequencing under this RFP?
Only sequencing assays are in-scope.

How is "sequencing result" defined? A genotype call or a FASTQ-like file?
The cost target does not include bioinformatics or data analyses. A FASTQ-like file is acceptable.

Can mosquitoes and ticks be used as environmental samples to screen for arboviruses? Or are only blood and fluid samples considered good for this RFP?
Sequencing from samples collected from mosquitoes or other vectors is eligible.

Review Process 

How does the review process work?
Please refer to the Rules and Guidelines document.

Can I get a list of potential reviewers who might be assigned to my application?
No. We do not make public the roster of reviewers.

Can I request that my application not be reviewed by a specific individual?
No. However, we will ask reviewers to self-identify conflicts of interest and will not assign reviewers with conflicts.

Will I receive specific feedback on my application if it is not selected?
Due to the rapid proposal and review timelines applicable to this RFP, applicants with proposals that are not selected for award may receive a notification of decline without specific feedback.

Can you provide more details on the independent evaluation?
This refers to independent evaluation of the assay itself (not the proposal review process). Promising assays that meet the cost and simplicity targets will be independently evaluated later, once ready, through a separate mechanism. Applicants do not need to include a budget for independent evaluation in their proposal - that will be a separate process.

What costs are allowable (equipment, compute, indirect costs)?
Refer to the budget template linked in the supporting documents and application portal, which lists eligible direct cost categories. For indirect costs, refer to the linked indirect cost policy.

Must the applicant or consortium already have access to a functioning sequencing laboratory and sequencing machine when applying, or can the award fund sequencing equipment, laboratory upgrades, reagents, and staff training?
The budget across all three tiers is relatively small and likely not sufficient to build full laboratory capacity from scratch, but such costs are not excluded. The budget should be determined by what is being proposed and what is needed to achieve the stated targets.

How could we determine the most appropriate funding tier for our proposal?
This is dependent on the readiness and scope of the proposed work.

Award Information 

Are grant awards made directly to individuals?
No. All awards are made to the organization where the individual holds their primary appointment. Institutions must agree to the terms and conditions governing each grant award prior to award activation.

How much money will each grant provide?
To accommodate different stages of innovation maturity, this RFP supports a tiered award structure, with funding levels and expectations aligned to the readiness and scope of the proposed work. Indicative award categories are:

Tier 1: Early-stage feasibility awards: up to US$300,000 (grant term up to 24months). For technically ambitious or higher-risk, earlier-stage concepts focused on feasibility testing, assay or workflow prototyping, and initial cost-reduction validation. Intended for approaches that require focused development to demonstrate viability.

Tier 2: Mid-stage development awards: up to US$600,000 (grant term up to 24months). For concepts with preliminary feasibility evidence that are ready to advance from prototype toward an integrated workflow—optimizing performance, broadening assay or pathogen coverage, and generating more robust cost-reduction and performance data.

Tier 3: Advanced development and validation awards: up to US$800,000 (grant term up to 36 months). For more mature concepts aimed at workflow refinement, performance optimization, and generation of proof-of-concept and validation data in relevant public-health use cases in LMICs.

We anticipate making approximately 15 awards across the three tiers. The final award amounts, number of awards, and funding mix will depend on proposal quality, technical maturity, funding availability, and strategic fit. Applicants should request funding commensurate with the scope and readiness of their proposed work and include a clear, milestone-based plan appropriate to the requested budget.

Indirect costs are allowable and should be included within the total requested funding (subject to the Gates Foundation's indirect cost policy).

Intellectual Property and Confidentiality

How can applicants protect their ideas and ensure confidentiality when sharing concepts in proposals? 
When submitting materials to the Foundation please keep in mind that because we have a focus on achieving charitable outcomes, we view information that we obtain through our grantmaking as a public good. Subject to the Gates Foundation's Privacy & Cookies Notice, the Foundation may also share information you provide to us (either orally or in writing) with third parties, including external reviewers, consultants, contingent workers, key partners and co-funders. You should assume that nothing will be kept confidential and should not include any information in the proposal, budget, supplemental materials, or reports that you consider proprietary.

Who owns Intellectual Property in funded projects?
Grantees retain ownership of intellectual property (IP) developed through foundation-funded grants. The foundation does, however, require that grant outputs be made widely available to the intended beneficiaries. You can read more here: Gates Foundation Global Access and IP Policy

Technical Support 

I forgot my password. How do I reset my password?
You can request to update your password within the application site. If you continue to have issues, please reach out to [email protected].

How will I know if my application was submitted?
Once an application is submitted, an email confirmation will be sent.

I'm having trouble uploading my application file. What should I do?
If you are having issues submitting your application, we would encourage you to submit from a different browser. If the issue persists, please email the specifics of your problem to [email protected].

How often do you intend to update the Frequently Asked Questions, and do you plan to provide answers to all questions submitted?
We will periodically post answers to questions as they are submitted, but do not have a specific schedule. We will provide answers on this page that are of relevance and of general interest to potential applicants. For answers to specific questions that are not covered here, please email [email protected]