During the 2014-2016 Ebola outbreak, Professor Christian Happi and colleagues used advanced genomics and deep sequencing technology to rapidly develop a new rapid five minutes diagnostics tests against Ebola Virus disease, within four months of the outbreak. The WHO and the US Food and Drug Administration (FDA) have since approved this diagnosis. He and his team have also worked to develop a novel five minutes rapid diagnosis test for Lassa fever. In addition to these major breakthroughs, Mr Happi discovered two new viruses (EKV-1 and EKV-2) in Ekpoma Edo State, using a new cutting-edge technology called microbial metagenomics, in 2015.

In this interview with Chiamaka Okafor, Mr Happi, a molecular biologist and Director of the World Bank-funded African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at the Redeemer’s University, Ede, in Nigeria’s Osun State, discusses the findings of a recent study from an advanced sequencing of the SARS-COV2 which shows that there are 3 lineages or strains of COVID-19 existing in Nigeria. This interview also explored the implications of these findings in containing the virus, as well as other speculations around the mutation of the virus. Excerpts:

Q: A recent genomic sequencing from your laboratory has shown the presence of three lineages of the coronavirus circulating in Nigeria

A: What we did was to use advanced sequencing technology, that is breaking the virus and having access to its entire DNA/RNA structure. We have a computational method, which we used to compare the virus in Nigeria to other viruses circulating in other places. We realised, three lineages are circulating in Nigeria (lineage A, B.1 and B.2.1); lineage A, is the original lineage which originated from Wuhan, China, this means some virus came directly from China; lineage B.1, the lineage that was circulating in Europe and also changed to lineage B.2.1 that is circulating in North America. So, we know, we have three sources of importation: China. America and Europe. This is a major finding from the data so far, I am sure when we look into more data, we probably will be finding more.

Q: Over time, we have seen studies about the virus’ mutation. Are there any such mutations from this study?

A: We realised that the virus has changed, a mutation. There was a particular mutation in the virus that was very important, that mutation is the D614G mutation; experiment, has demonstrated this mutation is associated with increased transmissibility, the virus is more infectious and also more pathogenic. We found that in four patients and three of them had severe diseases.

Prof. Christian Happi

The same mutation has been found in America and Europe; once this mutation occurs, the lineage with high transmissibility takes over and becomes the most predominant strain circulating and that is associated with severe diseases. We found this in four out of 20 samples analysed.

Once this highly transmissible and infectious lineage takes over the host, it is accompanied by severe diseases as it can evade immune interventions.

Q: Are there other findings?

A: One other finding that we did not report because we need to do more research on where it is happening, is the fact that the nucleic acid gene has a mutation and most of the primer (diagnostics) targets that particular gene. If the mutations are rising in that gene, it means the diagnostics will not be able to pick up or detect the virus and we will have a false negative.

Q: So when virologists talk of “false negative” how should the man on the street deconstruct such a scientific idiom?

A: Simply put, this is when the negative result from a test is not negative in the real sense. They are only negative because the diagnostic process has not picked up the virus due to its mutations though the virus is present.

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Q: What are the implications of these findings?

A: First, it is evident that the viruses in Nigeria came from multiple sources. When you have viruses from multiple sources living in the same environment, it means that there is a possibility of what we call recombination in virology (different virus meeting to exchange character over time). However, the changes, in this case, is not as fast as the flu virus. So, we are likely to have several strains of the coronavirus circulating.

Q: How does the foregoing affect the production of a vaccine?

A: Remember that the vaccine is developed in the laboratory. When designing the vaccine, you design something very specific to the sequence, but because the virus is evolving in the field and people, there is the possibility that by the time you are bringing your vaccine, the area that your vaccine is targeting would have changed.

Q: Does this mean we will never be able to get rid of the virus?

A: No. However, it is important to continuously monitor this because when you know this, you can quickly adjust your vaccine. So, instead of developing a vaccine that will only kill some strains, you update it to a vaccine that terminates all strains of the virus.

There is always an avenue to modify vaccines when changes occur.

Q: What will you say about the acclaimed new malaria symptoms losing the sense of smell and taste?

A: I do not know, but I think if you lose smell and taste that is definitely COVID-19, not malaria. Malaria does not come with such symptoms; people do not want to agree they have Covid, so they live in denial. Because people do not want to agree they have COVID-19, they claim it is malaria.