A lab assistant looks at an assay plate to prepare sequencing at the Wellcome Sanger Institute that is operated by Genome Research in Cambridge, Thursday, March 4, 2021.

From Congo to Chile, small labs are playing a growing role in global understanding of COVID

Scientists are tracking the evolution and spread of SARS-CoV-2 and developing critical responses to it. Efforts have ramped up a lot this year — thanks to a growing global network. 

The World

A lab assistant looks at an assay plate to prepare sequencing at the Wellcome Sanger Institute that is operated by Genome Research in Cambridge, March 4, 2021. Cambridge University microbiologist Sharon Peacock understood that genomic sequencing would be crucial in tracking the coronavirus, controlling outbreaks and developing vaccines, so she began working with colleagues around the country to put together a plan when there were just 84 confirmed cases in the country. 

Frank Augstein/AP

In March, the 1 millionth genomic sequence for the new coronavirus came from Chile; in late May, the 2 millionth from Mexico; in August, the 3 millionth from Singapore; and in September, the 4 millionth from Republic of Congo

Around the world, scientists have been racing to track the spread of SARS-CoV-2, since January 2020 — before it had a name. They’ve been doing this by sharing important genomic information with one another in near real time, through a global data science intiative, GISAID. It has now passed a big marker, holding more than 4 million genomic sequences — more than for any other pathogen. 

Related: India will soon roll out a DNA vaccine for the coronavirus. It’s the latest example of how COVID-19 is transforming vaccines.

“It was just work, work and work,” said Stephanie Goya, a scientist at the Ricardo Gutierrez Children’s Hospital in Argentina’s capital, Buenos Aires.

The hospital is home to one of the country’s main labs for the sequencing, surveillance and monitoring of COVID-19. 

Genomic sequences provide crucial information. Each time a virus infects a person, its code changes oh so slightly, like a small typo or scratch on a car. Sometimes, it changes in a more significant way. These details give scientists important clues about outbreaks, variants — and even vaccines and their effectiveness.

Yet, to make sense of what’s happening, even locally, researchers need data quickly, from all corners of the globe. 

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“This was a new virus, there’s no textbook on this virus, right? So we really relied on the global network."

Houriiya Tegally, researcher, University of KwaZulu–Natal, Durban, South Africa

“This was a new virus, there’s no textbook on this virus, right? So, we really relied on the global network,” said Houriiya Tegally, a researcher at the University of KwaZulu–Natal in Durban, South Africa. 

The efforts enabled Tegally and her colleagues to compare virus sequences from other places and make an important discovery late last year: the beta variant.  

“Just as we were doing our routine weekly sequencing and reporting, we started seeing some interesting and worrying variation in the genomes that we’re seeing from one part of the country,” she recalled.  

The group ramped up their analysis and noticed more cases were linked to this difference in the virus. Scientists elsewhere responded quickly, looking for traces of this variant, testing vaccines against it, and adjusting treatments. 

“It was happening right in front of our eyes, and the kind of surveillance that we were doing the past several months was finally serving a huge purpose,” she said.  

In recent months, that global network of scientists sharing information has expanded, with more and more labs developing this kind of capability. 

Related: Moderna to build manufacturing plant in Africa

“It has grown a lot,” said Christian Happi, a virologist who directs the African Centre of Excellence for Genomics of Infectious Diseases at Redeemer’s University in Nigeria. 

This past summer, Happi’s group, with the World Health Organization and the Africa Centers for Disease Control and Prevention, trained 20 scientists, hailing from Tunisia to Somalia to Rwanda, on how to do sequencing.

Happi estimates that now, at least half of the countries in Africa are able to do some level of local genomic sequencing. It’s a stark contrast to just a few years earlier during the West African Ebola outbreak when only his lab was able to do this. Scientists instead had to send their samples elsewhere, which can create critical delays in information. 

It might seem counterintuitive — that everyone is so willing to share their research with others around the world. It’s a delicate balance, Happi said. He and other scientists, especially in lower-income countries, worry their efforts could be exploited and used to make things like vaccines without any benefit to their communities.

“Unfortunately, we’ve seen also the situation whereby people have leveraged that data and created the solution, and refused to share the solution with those that shared the data."

Christian Happi, virologist and director, African Centre of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Nigeria

“Unfortunately, we’ve seen also the situation whereby people have leveraged that data and created the solution, and refused to share the solution with those that shared the data,” Happi said. “And that is definitely going to roll back this whole open data sharing and access principle.”

Other global genomic databases include ones based out of The European Bioinformatics Institute, the DNA Data Bank of Japan and the National Institutes of Health in the United States. They encourage submitting both raw and sequenced data without restrictions on how it’s used. 

GISAID, host of the most widely used platform for genomic sequences, is a nonprofit formed through an international group prepandemic, to track the flu. It requires that scientists get credit for their work if others use it in their own research. That goes a long way for researchers like Francine Ntoumi, founder of the Congolese Foundation for Medical Research whose lab was responsible for the 4 millionth-sequencing milestone. 

“This means that we participate in the game. We are able to say what is circulating. ... You are no more an observer, and I think it makes a difference.”

Francine Ntoumi, founder, Congolese Foundation for Medical Research

“This means that we participate in the game. We are able to say what is circulating,” Ntoumi said. “You are no more an observer, and I think it makes a difference.” 

After lots of work to build the infrastructure and raise funds, her group started sequencing this past June. Ntoumi said the information they’ve been able to gather — like the realization that the more transmissible delta variant is present — has been invaluable. 

She would like to do even more analysis, but a major challenge there — like in other lower-income countries around the world — is access to the technologies. The supply chain is very limited. It means that the ingredients needed to do the sequences, for example, must all be imported. That costs three to four times more compared to what it would in Europe or the US, Ntoumi said. 

Compared to the more than a million sequences that places like the United Kingdom have shared with the world, the sequencing of a few hundred samples in Republic of Congo might also seem like a drop in the bucket. Yet, Ntoumi and others say it’s filling in crucial blindspots for their communities and the world.

The significance, that a small lab in central Africa helped reach this global milestone of 4 million sequences, is not lost on her. She hopes that momentum continues to build globally as scientists prepare for future variants and viruses. 

“We were very happy, very happy,” Ntoumi said. “You contribute your information to global science.”