Nigeria’s disease detectives – epidemiologists and virologists – have been on a knightly mission to rescue Africa’s largest populace from the deadly pangs of COVID-19, a disease that has brought some of the world’s best health infrastructures to their knees.
Underfunding and under-capacity have long been the clog in the wheel of the health sector, yet these public health experts in no time activated their arsenal of technological resources and expertise the moment the first patient of coronavirus was reported in Nigeria.
Rosemary Audu, head of virology at the Nigeria Institute of Medical Research (NIMR), Lagos, was keeping an eye on locally-borne infectious diseases when coronavirus began to attract global attention.
So was Christian Happi at the African Centre for Excellence for the Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State.
But once the first COVID-19 case was confirmed in Nigeria, Happi led the team that mapped the genetic makeup of the virus through genome sequencing in 72 hours, between March 1 and 3, 2020.
That investigation became the first genome sequencing of SARS-CoV-2, the virus which causes COVID-19, in Africa. The time frame was the fastest in the world, compared to what had been done in China and some European countries.
A team of epidemiologists and virologists at the ACEGID lab did the mapping in partnership with the Nigerian Centre for Disease Control (NCDC), the Centre for Human Virology and Genomics (CHVG), Nigerian Institute of Medical Research (NIMR), the Centre for Human and Zoonotic Virology (CHAZVY), College of Medicine, Lagos University Teaching Hospital (LUTH), and the Lagos State Ministry of Health Bio-Safety Level 3 (BSL-3) Bio-Bank facility.
Genome sequencing is considered the most important factor in understanding how a disease behaves and how it can be used to develop a vaccine.
While this feat was reported widely in international science journals and a few local news outlets, it passed unnoticed among the general public. Nigerian scientists, despite that, placed the country at the forefront of using genomics as means to address infectious disease.
“There is nothing you can do in diagnosing this virus if you don’t understand the genetic makeup,” Happi, 51, explained to BusinessDay in a phone conversation. “You need the genetic makeup to develop any diagnostics. If you want to develop a vaccine, you need to understand the genomics in order to do it. So a countermeasure cannot be developed without understanding the genetic makeup of the virus.”
The Harvard-trained professor of Molecular Biology and Genomics said Nigeria was nearing development of a vaccine against COVID-19 as his lab was working on one based on the genomic mapping.
His lab is also developing a new diagnosis for the virus in efforts he said would make Africa a producer of scientific knowledge, rather than the consumer it has been for too long.
For him, it’s important that Africa creates centres of excellence where young talents in the diaspora can feel comfortable to produce new scientific knowledge locally.
As fight against the coronavirus scourge tightens, Happi said Nigeria is still on the ascending curve and yet to reach the peak, which is expected at some point next month, before a slowdown sets in.
Scientific strides despite difficulties
Despite a dilapidated and neglected health sector, genomic research has been with Nigeria for as long as times predating the first Ebola case in the country.
“There is nothing you can do in diagnosing this virus if you don’t understand the genetic makeup,” Happi, 51, explained to BusinessDay in a phone conversation. “You need the genetic makeup to develop any diagnostics. If you want to develop a vaccine, you need to understand the genomics in order to do it. So a countermeasure cannot be developed without understanding the genetic makeup of the virus.”
Chikwe Ihekweazu, director-general, NCDC, and his team were tackling an outbreak of the deadly Lassa fever when COVID-19 exploded in China.
The Centre for Human Virology and Genomics (CHVG), NIMR, had been sequencing HIV and had expanded to include some other viruses. In November 2019, five of its staff had gone for training at the Institute of Infectious Disease at Beijing, China, and the Senegal Research Institute, Dakar. They returned with new methods for genomic testing.
So as of January, NIMR didn’t foresee coronavirus but it had prepared for any viral outbreak since November last year.
When coronavirus outbreak was reported in the country on February 27, the institute specifically got primers for it, after receiving part of the samples. They tested and it turned positive.
“It worked and then we went ahead to sequencing, comparing it to the original strain that was reported in Wuhan. We found that it was 98 percent similar. We deposited it in a gene bank, just like a financial bank or a blood bank,” Happi said.
“After that, we have also sequenced viruses from a few other samples. We are monitoring the virus to see if there is any mutation, which is if it is changing in our own environment. When it is changing, it could affect the diagnostic kits or even the treatment and vaccines,” he said.
Happi said ACEGID didn’t see the coronavirus outbreak as a rude shock because of the centre’s experience with Ebola.
Within a year establishing at the Redeemer’s University, the centre was able to use genomics sequencing and diagnosis to quickly diagnose the first Ebola case in Nigeria and substantially work with the NCDC to contain the outbreak in 2014.
It was unprecedented in the history of medical and public health that Africa could lead in this regard.
During the four months of the Ebola crisis, it was able to develop a rapid diagnostics test that could detect the Ebola virus within 10 minutes.
In 2016, it used its newly developed technology called microbial metal genomics as a way to discover two brand new viruses in Nigeria – Epoma I and Epoma II.
In 2015 and 2016, ACEGID developed the same kind of test for Lassa fever, and afterwards used it to detect new outbreaks of Yellow Fever in Nigeria.
Previously handled infections including Ebola, Lassa fever, among others spurred the capacity development in genomics, serving as an avenue to test the capacity of molecular laboratories available in the country.
This effort has been possible with public and private researchers making the most of lean funding of the health sector.
Over the past decade, Nigeria’s health indicators have remained stagnant as one in eight children die before their 5th birthday. Less than one in three have received all basic immunisations, accounting for the highest number of children in the world who remain unvaccinated against measles.
The health sector is plagued by an inadequate number of trained health workers in rural and remote locations.
Government’s inability to commit more than 4 percent of total budget to health despite pledging 15 percent under the Abuja Declaration and delays in releases largely widen the gaps filled by international donors including Gavi, the Vaccine Alliance, Global Financing Facility of the World Bank, UKAID, Global Fund and the US Center for Disease Control and Prevention (CDC), among others.
Average individual spending on health in Nigeria was just about $5 in 2018, according to the World Bank, where the WHO estimates suggest at least $105 per person to deliver a basic package of health yearly.
Out-of-pocket health expenditure in Nigeria was 75.6 percent of total health spending in 2016 – a system which punishes the have-nots and pushes families into poverty when illness strikes.
Science has never moved so fast.
Since the NIMR developed a platform for testing for coronavirus cases on February 24, it has consistently picked positive cases.
“It is very infectious. People are just getting infected without symptoms. Once an individual gets infected, it could take up to 14 days to develop antibodies and those two weeks are the most infectious times,” Audu of NIMR told BusinessDay.
The speedy fashion of infections like coronavirus has prompted changes in the way viral diseases are tracked. This is why Nigeria’s epidemiologists are using the technology of genome sequencing to prevent further spread and create a vaccine.
Sequencing capacities these days have developed from what was obtainable when AIDS was first discovered. Epidemiologists can now answer disease questions –recognition and association – at a speed they could only fantasise about at the start of the AIDS epidemic.
The latest advances in the technology mean they can map viruses in a matter of hours or days, like Happi did. That speed and cooperation have been a game-changer, enabling this “genomic epidemiology” to be used in real time as the COVID-19 pandemic unfolds.
“We have used genomic epidemiology in other contexts where we were getting sequence in a month or a few weeks, but we’ve never had anything where we’ve had such fast turnaround or the number of sequences being shared from so many places so quickly,” said Emma Hodcroft, a genetic epidemiologist at the University of Basel in Switzerland.
As the global race to find a vaccine for the virus ramps up, the achievement of scientists based in Nigeria, who have made their findings public, will help speed the process of finding a cure to the disease. It will also give the country a foot in the door when a vaccine is discovered.
As of April 25, NCDC had ramped up molecular laboratories to 15, with three in Lagos, two in Abuja, and one each in Sokoto, Kano, Kaduna, Plateau, Oyo, Ogun, Osun, Edo, Rivers and Ebonyi States.
It aims to leverage capacity within the high throughput HIV molecular testing laboratories and private laboratories to increase testing capacity. This is expected to increase national testing output from 3,000 tests a day to at least 5,000 tests per day.
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