"The idea of pathogen sharing is based on power dynamics": Q&A with Senjuti Saha

Newsletter Edition #87 [The Weekly Primer]

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Hi,

We are very pleased to bring you a comprehensive, lively interview with Senjuti Saha, a Bangladeshi scientist with lucid views on pathogen-sharing and access to benefits, as seen from the field.

Divya Venkatesh, a researcher in viral evolution, also a Fellow with Geneva Health Files this summer, spoke to Saha in this important interview at a time when there is near unquestionable emphasis on the sharing of pathogens. Read on and share this.

Pathogen sharing is one of the key drivers of the discussions on the need for a new legal instrument to address future health emergencies.

Check out our exclusive story from last week: Threats of sanctions from Berlin ahead of talks in Geneva might alter support for the pandemic treaty. Consider subscribing to read our exclusive analyses. This will also support our reporting costs.

Until later!

Best,

Priti

Feel free to write to us: patnaik.reporting@gmail.com or genevahealthfiles@protonmail.com; Follow us on Twitter: @filesgeneva


I. THE GENEVA HEALTH FILES INTERVIEW

By Divya Venkatesh

"The idea of pathogen sharing is based on power dynamics"

During an outbreak, accessing pathogen samples and sequencing data easily are critical for designing effective public health responses and developing medical products. The norms that govern the sharing of pathogens in “peace” times, will have consequences on how samples and information are shared and compensated for, during outbreaks. Despite the growing chorus for sharing pathogens, this fundamental requirement that has not been discussed enough.

We spoke with Senjuti Saha, a well-known Bangladeshi scientist who works at the intersection of Clinical Microbiology and Public Health. Saha works at the Child Health Research Foundation (CHRF) in Dhaka. She is also a board member of the Polio Transition Independent Monitoring Board (TIMB) of the World Health Organization (WHO). She leads the genomic sequencing of SARS-CoV-2 effort in Bangladesh.

In this wide-ranging interview, Saha discusses with rare candour, the challenges, frustrations, the excitement, and determination that researchers like her, face in their quest to contribute to science and shape global health practice in significant ways.

As calls for a pandemic treaty continue to gain traction, driven by a need to make it binding for countries to share pathogens, she raises a fundamental question: “Do we really need to share pathogens?”

Read on to know more on why capacity building in science should go hand in hand with capacity building in policy-making.

[GHF] If you are (or have been) involved in sharing pathogen samples and sequences internationally, especially during outbreaks, what has been your experience as a scientist in a low- and middle-income country?

With pathogen sharing, there are two times we live in - peacetime and wartime. Now we are at war time; how we act depends on our experiences during peace times. Oftentimes, I'll get comments such as: ‘this is a pandemic; this is a wartime situation, you have to share everything that you have. And yes, we are ready to share everything that we have. But my decision and my trust in the system is all based on my experience when I was not in a pandemic/outbreak.

Sequencing isn't very common in Bangladesh. It's quite a new thing and most of my experience with sharing pathogen sequences comes from COVID-19. We run a SARS-CoV-2 genome surveillance initiative in Bangladesh, so we are constantly sequencing. We upload all our data on GISAID in real time, and we feel really good about it. We feel like we are contributing to the entire world, and to the scientific community.

Before, we had collaborated on, for example, Chikungunya sequencing. Bangladesh had a huge outbreak in 2017, and I was collaborating with the Chan Zuckerberg BioHub in San Francisco, USA. I shared the viral samples and they sequenced for us. I and it was a wonderful experience. We owned all the data, and l we learned how to analyse sequencing data in the process. That experience is helping us now.

With bacteria, we have had two different experiences:  in some cases, it was really good and helped us build capacity, even if they didn’t lead to really big publications. We have also had bad experiences. We ran this huge study on understanding infections in new-borns with collaborators. The primary investigator was from a high-income country, and we sent clinical samples to them for sequencing. [Our thinking was], take our pathogens, sequence them - it's good for the world. But every time we asked for the data, they asked us “What are you going to do with the data? We haven't published yet.” It's our pathogens. And we are not asking for all sequences, we are just asking for sequences from the bacteria that were isolated by our team in Bangladesh. I even made the case that we will not publish anything without talking to them. I had just come back to Bangladesh [from Canada] and I was training my team to analyse sequencing data and I wanted to use the data to teach. To date, we haven’t received our sequencing data and it has been probably three or four years. So, this is one end of the experience. But on the other end, are my experiences with other groups who have been absolutely wonderful.

Another problem I have faced is kind of in the grey area because I think people are trying to do good, but somehow it doesn’t end well. Recently, a collaborator institute sequenced a lot of our bacterial genomes, and suddenly, we found sequences of our pathogenic bacteria online. We wondered how that could happen when we hadn't released the data yet. And then we realized that it was because the funder of this institute had mandated quick sharing of all sequences.

[GHF] So are you saying that they did not take permission when they were supposed to?

This was a multi-site project, and the idea was that we would send our DNA [samples] to the sequencing institute and we would together sequence and publish it ... at some point. The Principal Investigator [PI] might have signed some agreements, but even then, it wasn't really clear that we didn't have any time to analyse [the data].

The biggest lie we tell ourselves is “I agree”, every time we update our software or whatever it is. We had no idea that we would not be the owner of this data and they would all be published online in NCBI. Even our names weren't there. It is no one's fault because I think it's just how the system is set up: you sequence using certain donor’s money, and they automatically go through a pipeline and become public.

[GHF] On a related note, can you talk about your experience with GISAID? Like you just mentioned, some researchers have said that they don't know what they are signing up for.

Yes, concerned colleagues have reached out to me to ask if we really understand how GISAID might share your data because nothing is clear from their website. And really, I don't know what I'm signing up for. All I know is that everyone is using GISAID to share data. It seems to be helping, so we will share, and hopefully, encourage others to share so that there is a global repository of data. At the same time, we are constantly scared, right? Every time we upload, we feel good about sharing the data, but will we ever be able to publish it? Or you know some armchair epidemiologist sitting somewhere, who is not really doing the studies, but this person will have access to all the data and will publish. And not only publish, maybe take some of the data out of context - because they have no idea how the sampling and sequencing was done and that can actually be more dangerous for us. So, these are some of the concerns that we have.

I fully believe that data sharing is beneficial. I encourage all my team members to share data. But there must be a difference between, let’s say when the University of Oxford shares data and when my team in Dhaka shares data - I don't have comparable computational resources. My team just doesn't have the time and energy, due to a lot of barriers that are non-existent in resource-rich settings*. We run studies and we analyse our data. We also don't have the same amount of expertise, so it takes us a lot more time. We're not saying we won't share our data, we’re just saying, give us more time.

[See also: Towards making global health research truly global. Lancet Global Health.]

[GHF] Have you been scooped?

Oh yeah, my team has, and for so many reasons, not only data sharing. You know how long it takes us to get reagents? We come up with an idea of, let's say doing a PCR for differentiating pathogens. And by the time the reagents (e.g., primers) come to Bangladesh, someone has already done the work, or my team has lost interest. I work with a really young team and they are very impatient. When they come up with an idea and they cannot do it within the next few days/weeks, they move on.

Still, you know with GISAID we kind of come to terms with it because at least in LMICs, I think we still believe we're in this together. However, there needs to be better governance.

[GHF] How do you see the trade-off between rapid and transparent sharing of pathogens and their genome sequence data, and the benefits for countries with limited research capacity/resources who share this information during outbreaks? Which benefits do you think are critical and deserve more focus?

All I will be talking about here are lived experiences – I don’t know if there’s any evidence for any of this. The benefit that I really see is – as a country, we haven't ever sequenced so much. There were sequencing machines here for years, but they were still in boxes or in bubble wraps. They have come out of boxes and people are sequencing now. And every time they upload, there will be a Facebook post about uploading to GISAID, and I think that's beautiful because that's rewarding people, they feel proud. But is this sustainable? 

So, we were actually just talking about other incentives or benefits that scientists in LMICs can get - can there be a credit system, for example. When you publish a paper, it's very rewarding and also that is our currency in academics. But what do you get out of sharing data? Other than oftentimes getting scooped by other scientists? Are these contributions taken into account when young scientists are applying for jobs or a grant? Are they asking how many genomes you have sequenced? And how much of the sequencing data have you shared openly?

Right now, our incentive structure is completely based on publications and grants, and we will always be behind if that does not change. And also, there should be acknowledgement of all the teams who are uploading to databases like GISAID in publications.  But I don't know how much of that happens in real time and who keeps track of it. I think GISAID needs to stand up and say, ‘you have to contact the author and get permission, no matter where that author is from’.

[GHF] Do you know of any labs in Bangladesh or other LMICs where a lab has been financially compensated specifically in exchange for sharing sequences (e.g., according to the Nagoya Protocol)?

No, I do not. That would be nice, right, because half the time we have no money for sequencing. We try to get money from other projects or grants. If I got incentivised to sequence, I would be sequencing more.

[GHF] Sort of like an Open Data financial fund?

Right. And in the form of incentives as well, for academics. We don't make much money but some kind of reward or being honoured in some way is important.

[GHF] What about capacity building?

Yes, another important aspect is capacity building. Despite all the rules and incentive structures we try to build, if real efforts are not made for in-country sequencing analysis, in-country storage of that data, developing in-country computational resources... At some point these countries will probably just stop sequencing.

It’s also really important to consider how to link all of that data to public policy. In high-income countries policymakers use the sequencing data for policy decisions. Our scientists are doing all that work, but we don't really know if our policy makers are taking sequencing data into account. So, capacity building is important not just in the science aspect but also in the policy-making aspect of public health.

[GHF] As a result of COVID-19 and the way it has contributed to the increase in sequencing, have researchers in Bangladesh started sequencing more, especially other pathogens in addition to SARS-CoV-2?

Really, really good question. And this is [what] we are trying to advocate for because now we know we have the capacity. We started sequencing way before COVID-19, so we are continuing to sequence other pathogens as well. But I don't know any other lab who's sequencing anything else other than SARS-CoV-2 right now. But that is what we are hoping - that we will start sequencing other pathogens e.g., pathogenic bacteria and dengue virus, which is a big killer in our country. Not only sequencing, if we can even use the capacity to test for more viral pathogens using the qPCR (Quantitative Polymerase Chain Reaction) machines that have been brought into the country and the hundreds of people who have been trained to use them, [that would be] amazing. That just might be a real silver lining in the near future.

I used NextStrain and saw how many SARS-CoV-2 genomes have been sequenced from the entire world compared with how many dengue virus sequences we have available from the entire world and it's very sad. The contrast is stark. COVID-19 will come under control, no matter what, but there are other epidemics we live with – we need to give more attention to them.

[GHF] Do you have any views on the inclusion of genome sequence data in existing pathogen sharing frameworks such as the Nagoya Protocol? What do you see as the role of existing genome sequence databases such as GISAID in the governance of pathogens and benefit sharing going forward?

I have actually never used the Nagoya protocol. I know Bangladesh signed it a while ago, but by the time it was put into practice, I think our group decided that we had our own sequencing capacity so we would just do the sequencing and analysis ourselves [instead of sending samples abroad]. So, I don't have much experience with that, but I have heard at various meetings that people have mixed feelings. [They don’t like] how long it takes, and how it's really, really bureaucratic.

It's just hard to find a middle ground that is ethical and equitable. Barriers don't only come from governance of the Nagoya protocol but also from how things are done in each of the countries - including the government of each country. These are difficult pathways and honestly, I don't know the solution. I don't know if anyone does. But every time the WHO is involved, you think - that's great, the WHO is involved… but it's going to be so slow!

[GHF] Do you believe that pathogens & benefits sharing mechanisms need to be improved?

I think this entire idea of pathogen sharing is based on power dynamics. Ideally, pathogens should only be shared in the rarest occasions, and the focus should rather be put on building capacity. Does the US share pathogens, does the UK? No, because they have the capacity. They have the money to do all of [the analysis] in their own country. So before sharing anything, there should be conversations about -- how do we not share? And only in the most urgent and necessary cases should pathogens be shared, with complete transparency and open documentation of why they are being shared.

It’s also worth noting who's doing the sharing and who is actually benefiting. There is a beautiful paper about this, published in Science a couple of years ago which said that all of these rules about open data sharing have always benefited the rich and it's just a mirror of the colonial aspect of global health. And I think this idea of pathogen sharing is very similar.

[See also: Open data sharing and the Global South—Who benefits?]

Coming back to COVID-19, there isn’t a problem with lack of sequencing data because it's a pandemic and the pathogen travels so fast that whenever we see a variant of concern emerging in one place, it quickly spreads around the world. For other endemic pathogens, it's not so fast.

The diversity of bacteria such as Streptococcus pneumoniae, the primary cause of pneumonia and meningitis, is very high across the world, as it is for Neisseria meningitidis, another bacterium that causes meningitis and is lethal. Since only high-income countries have the capacity to sequence, vaccines for Neisseria meningitidis have been designed according to the sequencing data that were available from those countries. So, when it was time for vaccine roll out and looking at vaccine efficacy and estimating vaccine efficacy, it was found that the vaccine will not be optimal for the Bangladeshi population. So even for high-income countries, it can be a waste of resources.

[GHF] What are your views on the new WHO biohub initiative? Do you think it is a step towards equity in pathogens sharing and access to benefits in global health?

I actually did not know about the Biohub. I only read up after you emailed me and it's great that there will be some governance [in pathogens sharing], and it won't be just one country sending to another country without any oversight. So, it's good, if I understand this properly, that everything will happen through WHO. That they will also take care of the risks associated with pathogen sharing etc. However, I don't see a capacity-building part in this entire thing, which worries me.

Like this interview? Write to Senjuti Saha here: senjutisaha@chrfbd.org and to Divya Venkatesh here: divya.venkatesh42@gmail.com

If you are interested in syndicating this interview, get in touch with us.

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II. POLICY UPDATES

- Declaration of the G20 Health Ministers

Also see: Opening remarks by WHO Director-General Dr Tedros Adhanom Ghebreyesus at G20 Health Ministers Meeting in Rome, Italy

Health Policy Watch: Bilateral Deals Will be Key to Nailing Down G20 Health Ministers’ Declaration

- Strengthening Global Health Security and Reforming the International Health Regulations: Making the World Safer From Future Pandemics by Antony J. Blinken and Xavier Becerra

- Biden seeks $65bn to deal with future pandemics: Financial Times

- More Than A Billion Available Stock Of Western Covid-19 Vaccines By The End Of 2021: Airfinity

- Brazil's Bolsonaro signs law that could break COVID-19 vaccine patents

- MSF demands Cepheid justify inadequate price reduction of COVID-19 tests

- India calls for an early outcome on TRIPS Waiver discussions

- Inauguration of the WHO Hub for Pandemic and Epidemic Intelligence: WHO

- The Future of Global Pandemic Security: Navigating shifting landscapes – a Gavi White Paper: Gavi


III. WHAT WE FOUND INTERESTING

Rithika has lined this up for you:

NEWS:

FROM THE JOURNALS/REPORTS


IV. WHAT WE ARE WATCHING

  • Launch of Airfinity report at the IFPMA briefing: September 7


V. OBITUARY

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