While countries are surfing deeper into what COVID-19 variants are circulating and their impact on vaccine efficacy, inadequate capacity for genomic sequencing has left Nigeria working with a dim vision of evolving events.
Africa’s largest economy has not found answers yet to the relationship between rising transmission, severity or mortality and the P681H, a Nigerian variant detected in January from samples collected since August and October 2020.
The alarm of a new variant raised in the UK was the prompting that jerked the Nigeria Centre for Disease Control (NCDC) into sequencing some samples, which later revealed that P681H shares at least one mutation with the UK variant B1.1.7.
Read Also: Now, Nigeria has 54 cases of the variant largely imported.
But genomic surveillance in countries monitoring the pandemic more closely indicates that tracking the virus changing patterns is more than a flash in the pan.
From South Africa to the UK, a robust volume of sequencing capacity is being deployed to study circulating variants. The results influence public health interventions and policy decisions such as which host communities should be on lockdown or what groups should be prioritised for monitoring.
Following the outbreak, the UK in April 2020, for instance, established a COVID-19 genomic consortium for rapid-research-response under a ‘fighting fund’ of £20 million.
The consortium has delivered 295,327 rapid and whole sequencing of SARS-CoV-2, the virus that causes COVID-19 pandemic to public health agencies, the NHS, and the UK government.
Feeding the consortium comes from the sequencing and analysis capacity of 41 facilities including 16 academic partners mostly universities, the Wellcome Sanger Institute, the four public health agencies of the UK, four Lighthouse Labs, and 16 additional sequencing labs.
For a population of 66.6 million, they sequence a proportion of all positive cases to determine how the virus behaves, allowing variants to be picked up in communities.
The country has established the possibility that being infected with the variant that was first identified in the UK is 30 percent more deadly compared to an earlier version of COVID-19 that was circulating, although the absolute risk of death is still low.
Also, targeted testing and viral sequencing done at the University of Reading suggests that the new Nigerian strain can blunt immunity, helping the disease evade the antibodies that fight it.
Unfortunately, Nigeria’s estimated population of 206 million has only three labs with sequencing capacity serving its COVID-19 fight: the NCDC Reference Laboratory, Nigeria Institute of Medical Research (NIMR), and the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID).
Nigerian universities on the hand have been mute in the face of a major health crisis.
From an overall of 206 next-generation sequencing devices in Africa, Nigeria has a total of 18, when South Africa has the highest concentration of 79 on the continent, and Kenya 28, stated a new Lancet publication authored by scientists including John Nkengasong, Director, Africa Centre for Disease Control and Prevention.
Although the report found most capacities outside national public health institutes, the data reveal more private investments in sequencing infrastructure have flown to South Africa and Kenya more than Nigeria.
“While we do have genomic surveillance in a few centres in Nigeria, the relative difference is the scale versus the UK and even South Africa. It obviously implies a reduced likelihood to detect such changes when they do happen,” Chike Ihekweazu, director-general, NCDC, said during a press briefing by the World Health Organisation, Africa Region.
“We really must learn from efforts in South Africa where they have both done sequencing to scale but also overtime. It is only when you do this over time that you can demonstrate changes in the prevalence of one variant over another.”
In South Africa, the data from genomic sequencing was taken a step further to detect that Astrazeneca vaccines had limited efficacy against the new South African variant, prompting the government to switch to Pfizer and Johnson & Johnson vaccines.
Although Nigeria has been picking pockets of cases of variants circulating around the country, limited capacity for genomic sequencing still leaves much to be discovered including the rate of distribution.
A survey by the NCDC already suggests data on infection rate, severity, and mortality could have been underestimated, giving a hint of how much information the country does not have about the virus.
“Not knowing the source or origin of a variant or how it is spreading within your country only means you are running blindfolded after the epidemic,” Oyewale Tomori, a professor of virology, told BusinessDay.
“On the vaccine side, you do not know which vaccine will be more effective because in the first place you do not know what variants you have and how distributed. So, you see without adequate sequencing you are both blind and deaf to the epidemic and your response will also be.”
Scientists highlight the need to increase capacity in national public health institutes and create functional networks with academic and research facilities and between countries.
