Where Are The SARS-CoV-2 Genomes From East Africa? – BioTechniques.com

The first reported case of COVID-19 was 13 March 2020 in Kenya and 10 weeks later, not a single genome is available publicly from any of the East African Community countries (Kenya, Tanzania, Burundi, Uganda, Rwanda, South Sudan). Why is it so? And why does it matter? Globally the main focus during this outbreak has been rapid COVID testing and not whole-genome sequencing. The team at Nextstrain has highlighted the utility of whole-genome sequencing in addition to rapid testing. We have presented below some of the challenges to obtaining whole genomes in East Africa and most importantly we have suggested a way forward.

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As a diagnostic, whole genomes are critical. Sequences confirm the identity of the disease-causing pathogen and can be further used for studying diversity, tracing movement of virus strains, designing models that can predict the disease spread and to better understand the enemy. A recent French study in bioRxiv has claimed the SARS-CoV-2 strain in France was not imported from China. This highlights the importance of a sequencing initiative to be able to properly trace the progress of the pandemic in every setting the Icelandic approach.

Real-time data are very important because they serve as a diagnostic test that guides quick patient management and decision-making from an epidemiological standpoint; and genomics would provide further tools in designing therapeutic approaches.

Over the years, millions of USD have been spent building genomic sequencing facilities in East Africa. In Kenya, Biosciences for east and central Africa (plant and animal) and KEMRIWellcome Trust (both Nairobi, Kenya) (human health) are partnerships with national governments and international funders but to date neither have delivered a genome.

In Uganda, the Uganda Virus Research Institute (UVRI; Entebbe, Uganda), is a centre of excellence in virus research with the human and infrastructural capacity and international support for genome sequencing. However, UVRI has also not yet delivered a single SARS-CoV-2 genome.

Tanzania has a different landscape. There are no large international sequencing facilities, but the national research organizations, universities and hospitals like Muhimbili National Hospital (Dar es Salaam, Tanzania) and the Sokoine University of Agriculture (SUA; Morogoro, Tanzania) have various platforms such as the Illumina (CA, USA) MiSeq, HiSeq and the Oxford Nanopore MinION. They too have not yet generated any SARS-CoV-2 genomes.

So why have none of these institutions with the sequencing infrastructure and support in Kenya, Tanzania and Uganda not delivered the much-needed SARS-CoV-2 genomes yet?

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For Kenya, the biggest hurdle is a lack of partnerships. So far, all the work on COVID-19 is handled solely by the Ministry of Health (MoH; Nairobi, Kenya). Accordingly, there has been no access to samples considering also that this disease is highly infectious and these samples need to be handled in biosafety level 4 labs. Due to poor partnerships (aka poor coordination), the work is largely being done in KEMRI and private medical labs such as Lancet. The other limitations are:

Power, computers, internet and PCR machines are not a challenge.

The sequencing capacity is there especially in research and academic institutes; the SUA has the Thermo Fisher Scientific (MA, USA) Ion Torrent that they use for foot and mouth disease and other animal research, the Kilimanjaro Clinical research Institute (KCRI, Moshi, Tanzania) has the Illumina MiSEQ (I have seen this personally) which they use for their tuberculosis research; the Government Chemist Laboratory Authority (Dar es Salaam, Tanzania) has a genetic analyzer and was able to acquire the Illumina HiSEQ, which they use for their forensic studies; the National Health Laboratory (Dar es Salaam, Tanzania) also has a genetic analyzer. There are two laboratories which are capable of sequencing using Oxford Nanopore Technologies (Oxford, UK). These are Muhimbili national hospital and the SUA in collaboration with the NHL. There were no funds to do the sequencing at the beginning of the outbreak but now the SUA has secured some funds to sequence, Muhimbili might get a donation to do so too. Another laboratory that is capable of sequencing but does not have the funds to do so is the KCRI. Capacity and skills are not a problem. However, in a government setting and in most institutes, employees are given specific tasks as per institute mandate. Its true that we have many people trained in sequencing, but some are outside government settings/employment and some of those who are in government employment are not in clinical research. For example, the cassava disease diagnostic team was focused on agricultural research. Some of the trained people are not trained to handle clinical samples. So clearly there is a disconnect between clinical and agricultural disease diagnostic techniques.

Another challenge is lack of local partnerships (internal collaborations among different institutes in Tanzania). There are no good networks that connect healthcare facilities with research and academic institutes. Most healthcare facilities do not have the critical mass of trained experts in sequencing and due to their mandates and the sheer heaviness of their routine workload, they rarely have the bandwidth to pursue research regularly. Herein comes the need to forge strong links between the two that would have been in prime position to address this pandemic. Unfortunately it has not been easy; from my personal experience there are a lot of territorial issues at play that are hard to overcome. Perhaps this pandemic might bring a change in mindset.

Another challenge is global but is felt more in countries like Tanzania; inadequate funding for R&D. While the government, through the Tanzania Commission for Science and Technology (COSTECH) and other institutes, provides for R&D funding, it is still limited especially when compared to the costs of running genomics experiments. External funding is always difficult especially for researchers who are not part of a consortium led by PIs from Europe and/or North America. This has helped establish centers but has meant that the moment funding runs out the lab is less active, the reagents and consumables run out and equipment ends up in disuse.

There appears to be a lack of awareness among policy makers and/or not enough initiative from the local scientists working in this field to inform our policy makers about the importance of whole genome sequencing for management of COVID-19. Since most sequencing initiatives in the country are led by foreign consortia (which we feel needs to change) led from either Europe or North America it is possible that the benefits from such projects are rarely seen by policy makers in Tanzania. We see there needs to be a clear link between the governments and local scientists to work on the same matters from different perspectives. We hope the donated research reagents to the African CDC will reach the institutes as soon as they arrive the airport without customs delays.

There is both human and infrastructural capacity in sequencing at UVRI and the Medical Research Council all based at Entebbe, Uganda. However, the COVID-19 genomes are not yet out in the public arena.

There are computers, access to internet, power and the supplies required to carry out PCR testing and analysis of coronavirus/COVID-19 infections, which were initially provided by the UVRI through its running projects and currently with the support of the government. However, more supplies would be needed to monitor the entry and spread of the virus in the communities.

As of today, it is the sole responsibility of the Ministry of Health (Kampala, Uganda) as the mandated institution of government to lead all COVID-19 pandemic-related issues. This includes checking for possible cases with suspected symptoms, isolation/quarantine, collecting samples, sample analysis and announcement of outcomes of testing and treatment. In addition, task forces were established to coordinate COVID-19-related issues at national, regional and district level. The laboratory analysis of the suspected COVID-19 samples is carried out by UVRI. Although there are other institutions with both human and infrastructural capacity in molecular biology and disease diagnostics, there are limited partnerships on widening the testing for COVID-19 in the country to involve the private sector. This may be partly due to the highly infectious nature of the disease and the requirement to carry out the laboratory testing and analysis in a biosafety level 4 containment facility such as UVRI. However, there are some partnerships within the private sector in management of the disease.

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This article is written by East African Scientists and international partners who have been working for years on collaborative research projects, including The Cassava Virus Action Project, around managing emerging plant virus disease pandemics using novel molecular diagnostics and genomics. The team was disheartened to watch COVID-19 arrive and spread in East African countries, where they have successfully partnered to build capacity in rapid plant virus diagnostics and genome sequencing using novel portable technologies such as the Oxford Nanopore MinION, which have not been put to good use in the fight against the pandemic.

Professor Elijah Ateka Molecular Biologist

Dr. Joseph Ndunguru Molecular Plant Pathologist

Dr. Daniel Maeda Molecular and Cellular Biologist (Health Focus)

Mr. Charles Kayuki Molecular Biologist

Dr. Peter Sseruwagi Molecular disease epidemiologist

Dr. Laura M. Boykin Computational Biologist

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Where Are The SARS-CoV-2 Genomes From East Africa? - BioTechniques.com