ONYANGO: Dealing with the Indian variant

Kenya must expand genetic sequencing throughout the country.

In Summary

•Importantly, A National-level analysis of this data should be done on a regular basis and findings made public.

•The government needs to invest and support more scientific and operational research on vaccine effectiveness.

Passengers being screened for Covid-19 symptoms.
COVID-19: Passengers being screened for Covid-19 symptoms.
Image: STEPHEN ATARIKO

Scientifically, a variant of concern (VOC) refers to a lineage of a virus that’s unusual in the sense that it has many more genome mutations than previously found in the preexisting variant.

The genomic mutation may affect the immune control and virulence. In addition, the VOC may rapidly displace the preexisting variants in a short period of time or lead to a rise in the R index, a measure of transmissibility, suggesting a high transmissibility.

Although opinions differ on how to distinguish between human behavioral and viral genetic contributions as causes for increased transmissibility in all populations; some argue that in the case of some SARS-CoV-2 variants, most evidences for increased transmission are indirect and do not prove that they transmit, in a virological sense, between hosts, recent research on Covid variants in India has suggested that genetic changes are important.

This is a major public health concern since a more transmissible strain would result in more cases, with a higher percentage of those cases resulting in severe disease requiring hospitalization and an increased absolute risk of mortality.

In the wake of the Indian variant, which is now more pronounced in the Nyanza region, we must tamper our obsession with ensuring optimal vaccination access with the realization that we should try to address both the VOC problem and the need for increased immunization rates. To do so, we need an exercise in foresight, anticipation, and a coordinated bio-defense response strategy.

According to Mercy Mwangangi, chief administrative secretary at the MoH, Kenya has invested in cutting-edge infrastructure to simplify coronavirus genetic sequencing and accelerate the discovery of novel variants.

In a January televised appearance, she suggested that the country has facilities that are well equipped to handle sequencing of the virus to help identify and report the new strains before mass inoculation kicks off at the end of February. The truth, however, is far more nuanced than the fanfare suggests. 

 If there's one tool in the pandemic response that we've been slow to adopt and haven't used to its full potential, it's genomic sequencing. Though the procedural steps such as establishing a genomic consortia at the KEMRI laboratories have been taken, sequencing has remained at a relatively low level, with only a few hundred cases sequenced.

The problem of a lack of genomic infrastructure is exacerbated by the slow pace with which data is shared. It’s no wonder that we don't know much about the Indian variant.

A successful Covid-19 pandemic response should include, among other things, keeping track of VOC and undertaking additional research into their transmissibility, immunological evasion, and ability to cause severe disease. That’s precisely what genomic sequencing entails.

When the US and UK's success in limiting Covid is highlighted, much credit is given to increased vaccination coverage; however, it's often forgotten that these countries have also scaled up genomic sequencing, tracked emerging variants, and used that evidence to take timely actions.

Kenya must expand genetic sequencing throughout the country. MoH should guarantee that sufficient and representative samples are collected to aide in tracking county-level trends in circulating variants.

Importantly, A National-level analysis of this data should be done on a regular basis and findings made public. The government needs to invest and support more scientific and operational research on vaccine effectiveness.

Let’s ponder over this: Given that the majority of persons who have received at least one dose of vaccines are over the age of 58, with only a few over 45, does this suggest that the goal of vaccination should be to attain saturation coverage of the high-risk population with both injections, rather than one shot to everyone?

Does it mandate a need for a reduced gap between two doses of the vaccine for anyone older than 45 years? Should the vaccination of those 18-44 be put on hold till vaccine supply is assured or should it be done only in counties where the the highly transmissible variants are predominant? And how do we deal with signs of immune evasion and decreased vaccination efficacy against the VOC? 

These are the questions that our experts must consider and address, and there is no better tool to do so than genome sequencing.

Charles Onyango, Life Scientist and Global Fellow Moving Worlds Institute [email protected]