Why COVID-19 surveillance in Nigeria is critical
The rise and fall of variant of concern eta in western Africa

Date:
February 3, 2022
Source:
Northwestern University
Summary:
If the United States ignores COVID-19 in Nigeria, we forgo global
genomic surveillance at our own peril, reports a new study.



FULL STORY ==========================================================================
If the United States ignores COVID-19 in Nigeria, we forgo global genomic surveillance at our own peril, reports a new Northwestern Medicine study.


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The study found global efforts to track variants grossly underreported
a probable variant of concern, eta, circulating in Nigeria in early
2021. This was followed by the circulation of a rare delta sublineage
in the region that was different from the delta variant that circulated
in most other parts of the globe.

"Nigeria is the seventh-most populated country on the planet, but
there was very little viral sequencing data available from Nigeria
until we started this study," said co-corresponding study author Judd Hultquist. "The concern in having these gaps in surveillance is there
may be new variants popping up in places across the globe we are not
seeing. We do not want to be caught unprepared if all of a sudden a new
variant with unique properties emerges onto the world stage." Hultquist
is associate director of the Center for Pathogen Genomics and Microbial Evolution at Northwestern University Feinberg School of Medicine. He also
is an assistant professor of medicine in infectious diseases at Feinberg.

"This study demonstrates the critical need for international cooperation
in infectious disease surveillance in undersampled regions for the
monitoring and 'early-warning' detection of new SARS-CoV-2 variants
with concerning potential," said Ramon Lorenzo-Redondo, co-corresponding
study author.

Lorenzo-Redondo is an assistant professor of medicine and the
bioinformatics director of the Center for Pathogen Genomics and Microbial Evolution at Feinberg.



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The study was published Feb. 3 in Nature Communications.

Northwestern scientists sequenced nearly 400 nasal swabs from Nigerian
COVID-19 patients, collected by collaborator Dr. Moses Adewumi and
his team at the University of Ibadan, who shipped the specimens to
Northwestern for sequencing and analysis. The Ibadan scientists did
not yet have the equipment or resources to sequence samples at their
own institution.

"What we found was really unexpected," Hultquist said.

'Gaps in surveillance leave us vulnerable' Northwestern researchers
discovered two different variants of the virus that emerged in Nigeria
at different times but that went largely underreported.



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"We showed one of those variants -- now called eta by the World Health Organization -- had all the characteristics of a variant of concern,"
Hultquist said. "The spike protein of the eta variant was more efficient
at promoting infection in vitro and enhanced viral evasion of neutralizing antibody responses following natural infection. Furthermore, eta was able
to outcompete the alpha variant in the region before the arrival of delta.

"When alpha was circulating, it was a major focus of concern for public
health officials and was widely reported in the media. But eta was more important in Nigeria and other West African countries, even outcompeting
alpha in these regions, and we completely missed it. These types of
gaps in surveillance leave us vulnerable. How long are we willing to
take the risk that an important variant pops up and we miss it until
it is already here?" Several other variants of concern, including beta
and omicron, are suspected to have originated from Africa, emphasizing
the importance of monitoring these undersampled regions. Scientists in
South Africa identified the omicron variant early on and warned it might represent a new variant of concern, enabling other countries to prepare.

"They were absolutely right," Hultquist said.

The differences in the types of SARS-CoV-2 viruses found in Nigeria
compared to the rest of the world suggests there is something about
the region that is driving the evolution of these unique variants,
which scientists don't entirely understand.

Very different viral dynamic is occurring in Nigeria. Why? "In this
study, we have observed repeated expansions of globally uncommon lineages
in Nigeria, which indicates a very different viral dynamic occurring in
Nigeria compared to other regions of the world," Lorenzo-Redondo said.

The country has reported relatively low numbers of hospitalization and
low numbers of deaths throughout the pandemic, despite low vaccination
rates and a population of over 200 million people. While it's possible the
low case counts and hospitalizations could be due to underreporting, the
number of deaths are thought to be more accurate. Part of the explanation
for this low mortality rate might be Nigeria's younger overall population,
"but most likely other complex factors not yet understood involving host immunity and/or virus-host interactions are playing a very important
role," Lorenzo-Redondo said.

"The fact that we have repeatedly seen bizarre variants pop up in Nigeria suggests the virus is there and in high enough numbers to be actively evolving," Hultquist said.

To identify what variants might be problematic, scientists rely on how
many times they see it and whether it is associated with increases
in cases, hospitalizations or deaths. But if a variant pops up in
Nigeria where there is little sequencing, scientists might miss early
warning signs. By the time it spreads around the globe, it's too late, Hultquist said.

"We have to start treating this pandemic truly as a global pandemic,"
Hultquist said. "This study demonstrates how our lack of a dedicated,
global genomic surveillance effort is resulting in skewed data with
potential risks. It's important to understand what new variants are
arising to inform best practices in clinical care and public health
policy." Collecting West African samples is currently too arduous But
many low- and middle-income countries need more support. The effort
required to obtain the Nigerian samples shows the challenges inherent in
these efforts. Researchers in Ibadan had to travel to Lagos, the biggest
city in the country, to obtain dry ice, sometimes driving between four and
10 hours in sometimes bad road conditions to do so. After they returned
to pack the samples in the ice, they then had to drive again to Lagos
to ship them to the U.S. for a total of four often arduous trips.

Better access to sequencing equipment, supplies and training would allow
more of the surveillance to be done in Nigeria. Building capacity for
this type of work in other countries remains a major goal for the Center
for Pathogen Genomics and Microbial Evolution and Feinberg's Institute
for Global Health.

This study was possible thanks to the long-term collaborative team led
by Dr.

Babafemi Taiwo, chief of infectious diseases at Feinberg, between
Northwestern University and the University of Ibadan.

Other Northwestern authors include Dr. Egon Ozer, Babafemi Taiwo, Lacy
Simons, Taylor Dean and Dr. Mamoudou Maiga.

The research was supported in part by the Northwestern Havey Institute
for Global Health, the Dixon Family Foundation and the Northwestern
Center for Advanced Technologies, the NIH-supported Third Coast CFAR P30 AI117943, NIH grant R21 AI163912, NIH grant U19 AI135964, NIH grant D43 TW009608, NIH Fogarty International Center award D43TW009608, NIH grant
R35 GM118187 and NIH-NIAID Center for Structural Genomics of Infectious Diseases award HHSN272201700060C.

.

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written by Marla Paul.

Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Egon A. Ozer, Lacy M. Simons, Olubusuyi M. Adewumi, Adeola
A. Fowotade,
Ewean C. Omoruyi, Johnson A. Adeniji, Oluseyi A. Olayinka, Taylor J.

Dean, Janet Zayas, Pavan P. Bhimalli, Michelle K. Ash, Almoustapha
I.

Maiga, Anou M. Somboro, Mamoudou Maiga, Adam Godzik, Jeffrey R.

Schneider, Joa~o I. Mamede, Babafemi O. Taiwo, Judd F. Hultquist,
Ramon Lorenzo-Redondo. Multiple expansions of globally uncommon
SARS-CoV- 2 lineages in Nigeria. Nature Communications, 2022; 13
(1) DOI: 10.1038/ s41467-022-28317-5 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/02/220203161210.htm

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