27 September 2022
Egypt’s SARS-CoV-2 sequencing challenges
Published online 7 May 2021
Researchers in countries like Egypt require more centralized support for their sequencing efforts.
The situation in India, where funeral pyres are being set up in car parks and social media is flooded with desperate pleas for oxygen cylinders, is a harsh reminder of what SARS-CoV-2 can do to a country. Some scientists blame this massive spike in new COVID-19 cases on the SARS-CoV-2 variant B.1.617, whose predominant lineage was first identified in India in December 2020. But sporadic and inadequate gene sequencing data for the virus has made it difficult to be certain of this association and thus help guide the public health response to deal with this surge.
Sequencing efforts are similarly limited across research institutes in Egypt, where published sequences represent less than 0.2% of the number of reported cases.
“There are individual sequencing efforts in Egypt in a few universities and research hospitals,” says Ramy Karam Aziz, head of the Microbiology and Immunology Program at the Children Cancer Hospital 57357. Every research effort is submitted individually to the global database or not submitted at all, as nothing compels researchers to submit the sequences they have, he explains.
When COVID-19 was declared a pandemic in March 2020, some research institutes in Egypt dashed to develop their infrastructure to sequence the virus from local samples. The main aim back then was to track and trace the virus to find out how it entered the country.
Ahmed Moustafa, professor of bioinformatics at the American University in Cairo, and his team were among the groups that worked on tracing the virus. Looking at the sequences sent to them by a research team at Ain Shams University, they assembled the genomes and compared them with the reference genome of the SARS-CoV-2 virus. “We concluded that the virus mainly came to Egypt from Saudi Arabia and the United Kingdom,” he says. Their study is yet to be published.
Aziz says local transmission tracing is no longer necessary, and the important thing now is to find out how the virus is mutating and changing.
“In some sense, every sequence is a variant,” explains Aziz. But some variants are significant as they appear to be more infectious. Identifying SARS-CoV-2 variants is a crucial part of public health surveillance to inform and guide the necessary precautions to contain new variants as quickly as possible. The UK, for example, has been especially vigilant in this regard. They quickly reactivated lockdown measures in certain areas as soon as they identified the B.11.7 variant and found it to be more transmissible. They were also one of the first countries to institute harsh quarantine measures for people arriving from South Africa as soon as the B.1.351 variant was identified.
For sequencing efforts to pay off, researchers need to sequence a large number of samples taken from positive COVID-19 cases. The UK has submitted around 400,000 sequence entries to global databases so far, which represents approximately 9% of all reported cases in the country.
Egypt, on the other hand, has only shared 410 SARS-CoV-2 virus sequences with the global databases. Aziz thinks it is unfair to compare countries to the UK and the US, which have contributed 31% and 28% respectively of the sequencing data currently available globally.
“Egypt’s COVID-19 sequencing efforts are average regionally and globally,” he says. Saudi Arabia, the largest Gulf Cooperation Council (GCC) country, has so far submitted 953 sequences, representing only 0.23% of its reported cases. The United Arab Emirates, the leading country in the Middle East and North Africa in sample sequencing, has submitted 1,846 sequences, representing 0.35% of their reported cases.
Sequencing efforts would need to be significantly enhanced relative to the number of reported cases for these and other countries to be able to properly track variants and identify new ones.
In Egypt and other countries, where technical expertise is not lacking, a myriad of other logistical challenges stand between researchers and their ability to enhance SARS-CoV-2 sequencing efforts.
Identifying SARS-CoV-2 variants is a crucial part of public health surveillance to inform and guide the necessary precautions to contain new variants as quickly as possible.
One of the biggest challenges is being able to gather geographically representative samples. Aziz explains that in Egypt, for example, more than 90% of the samples that have been sequenced have come from two main public hospitals in Cairo. This can inform researchers if the cases originated from a common source, but this is not essential information at this stage. “The question should be: do we have any new variants in Egypt different from the ones researchers have found elsewhere around the world?” he says.
Researchers are also finding it difficult to get hold of the reagents and chemicals they need to sequence the virus. When Moustafa was a researcher in the US, the company producing his reagents was next to his lab. “We could order what we wanted in the morning and receive it the same afternoon and continue our work,” says Moustafa.
In Egypt things are more complicated, as only one company imports reagents into the country. Coupled with bureaucracy, the necessary permits and slow customs procedures, getting hold of reagents is a long and arduous process that can take up to two months. “It is very frustrating when your work comes to a halt because of something like this,” says Aziz.
Aziz and Moustafa agree that Egypt is in need of an initiative that pulls together the scattered sequencing efforts in the country into a unified database. This sort of comprehensive screening programme would require strong governmental support and political will.
Aziz says this sort of a national effort, with a central entity organizing and facilitating it, would make this sort of research more routine and non-competitive. Sequencing samples is expensive work, he explains, with researchers currently expecting returns from their investment in the form of published studies.
“We have to find a different reward system for researchers doing this work other than publishing, to encourage them to continue working on it and submitting their data. It might come in the shape of incentives, recognition or promotion,” says Aziz.