Abuja – As COVID-19 continues to spread, the higher the chances of more variants emerging. Since the onset of the pandemic, four variants of concern have been identified, with the Delta—first detected in India—being the most transmissible currently and dominant in many countries. In Nigeria, Dr Chikwe Ihekweazu, the Director-General of the Nigeria Centre for Disease Control, explains how the country is responding to the pandemic in the wake of the more infectious variants.

How have COVID-19 variants affected the pandemic response in Nigeria?

The Delta variant is now the dominant strain in our country and has been found in over 90% of samples tested. When the Delta variant was initially detected globally, Nigeria acted quickly to introduce compulsory isolation of travellers from countries with high incidence of cases associated with the variant as an initial mitigation measure. We also revised our genomic surveillance strategy to sequence samples among travellers testing positive on arrival in Nigeria in order to catch variants quickly.

As the Delta variant began to spread in the country, the first step was getting the word out there fast to warn the general public. We scaled up our risk communications using traditional and social media. Another priority was increasing capacity to identify cases even quicker to stop the chain of transmission. We are now working with other institutions in Nigeria to introduce the use of Rapid Diagnostic Tests in public settings such as schools, youth service camps, government offices among others. Of course, we have also sustained other measures to protect those at greater risk, including supporting infection prevention and control in health facilities and providing training to health workers.

Nigeria is further strengthening genomic surveillance capacity to identify and quickly characterise emerging variants. The data from this also guides our policies such as compulsory testing for international travellers. We are also carrying out studies on vaccine effectiveness and contributing to global scientific evidence. We will continue to maintain a strong risk communications approach to ensure that Nigerians are aware of the risks presented by variants and continue adhering to public health measures.

How is Nigeria scaling up genomic sequencing?

Nigeria has contributed sequences in the global SARS-COV-2 genome repository maintained by Global Initiative on Sharing All Influenza Data. More samples are sent for sequencing than ever before, with 100% weekly increase in the number of samples sequenced. This is currently done by a network of five laboratories coordinated by the Nigeria Centre for Disease Control’s National Reference Laboratory. We are also rapidly scaling up capacity for increased testing to meet this need.

The Nigeria Centre for Disease Control is now looking to replicate our successful efforts in building Nigeria’s capacity for molecular testing of COVID-19 with capacity building for genomic sequencing. We are in conversations with our partners such as the United Kingdom’s Health Security Agency given their strengths in pathogen genomics. We are also receiving support from Africa Centre for Disease Control and Prevention, which is coordinating continental efforts to scale up genomic sequencing.   

These efforts are not only important for sequencing of SARS-CoV-2 samples, but for other pathogens that are endemic in Nigeria such as the Lassa fever and yellow fever viruses.

Other boosting genomic surveillance, how can Nigeria improve outbreak readiness?

In the last five years, the Nigeria Centre for Disease Control has worked very hard to strengthen Nigeria’s capacity to prevent, detect and respond to infectious disease outbreaks. We have built systems for coordination of outbreak preparedness and response through Emergency Operations Centres at national and subnational levels, established a network of public health laboratories coordinated by Nigeria Centre for Disease Control’s National Reference Laboratory, digitalized our infectious disease surveillance system, established new programmes for infection prevention control, risk communications, antimicrobial resistance and several other activities.

However, there is still a lot of work to be done. This will require strong commitment by the government, sufficient, stable and sustainable financing for health security and accountability to support these.

Improved outbreak readiness will also require strong collaboration — both with African countries and countries in other regions. This has been well illustrated by our response to the COVID-19 pandemic. We are grateful for collaboration platforms created by the World Health Organization, Africa Centre for Disease Control and Prevention and other partners to enable cross-country learning.

Why is genomic sequencing limited in many African countries?

There is clear inequality in sequencing capacity globally, and the need to scale up this capacity in African countries is very clear. For several decades, there has been limited focus and poor investment in genomic sequencing capacity – both from African governments and partners.

However, the path forward is to encourage and enable more countries on the continent to develop this capacity. There is proof from several models including the use of government, private and academic laboratories with coordination by national public health institutes.

We have begun to make progress with institutions in countries like South Africa, The Gambia and several others showing excellent progress. The Africa Centre for Disease Control and Prevention has also secured funding for pathogen genomics research and development through the Africa Pathogen Genomics Initiative which will support countries. The pandemic has brought to fore the inequality that exists and the risks we face if we do not develop genomic sequencing capacity in African countries.