Expanding the Capacity of Governments for Genome Sequencing in West Africa

Covid-19

Expanding the Capacity of Governments for Genome Sequencing in West Africa

Commentary
Posted on: 24th September 2020
By Multiple Authors
Philip Spencer
Governance Advisor, The Gambia
Abdul Karim Sesay
Genomics Facility Lead, Medical Research Council Unit, The Gambia

On 15 March, flight AT579 arrived at Banjul International Airport with 58 people onboard including the crew. At the time, The Gambia had registered no cases of Covid-19, yet following the arrival of the first case in neighbouring Senegal on 2 March 2020, the country was on high alert and information had begun spreading about the new virus. Two days after the flight arrived, on 17 March, the Government of The Gambia reported that one of its passengers (travelling from the UK) had tested positive for Covid-19. 

This news turned the country on its head, as the Ministry of Health went from methodical preparation into top gear with its response efforts, including contact tracing the other passengers from the flight. The close proximity and limited ventilation of modern aircraft raised expectations that other positive cases were likely to emerge. 

With news of a second case of Covid-19 from the same flight soon confirmed, experts felt as if their predictions had come true and that the aeroplane environment and its close corridors had instigated the transmission of Covid-19. However, this assumption proved incorrect. In fact, the virus carried by the first case originated from Europe, while that of the second case – where the infected person had originally travelled from France – had a version of the virus originating from Asia. Since the two passengers carried different strands of Covid-19, it is clear their arrival into the country on the same flight was merely a coincidence, not the source of infection. This important discovery was made possible by genome sequencing, done by scientists at the Genomics Core Facility at the Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene & Tropical Medicine (LSHTM).

Genome sequencing involves analysing the letters of a virus’s genetic code to track its mutations. Viral genome data allows governments and researchers to trace the origin of Covid-19 outbreaks in their jurisdiction and pin down the moment when community transmission occurred. Information from genome sequencing reveals the virus’ geographical spread, its comparability to other viruses, mode and tempo of evolution, and adaptation to human hosts. This vital information can be used to assist in epidemiological investigations, particularly when combined with other types of data (e.g, case counts). 

The first publication of a Covid-19 genome sequence occurred on January 11 and since then the online repository of sequenced and shared samples has risen to 107,000 viral genomes. In countries where Covid-19 restrictions such as borders closures are easing (like New Zealand), genome sequencing is playing a critical role in identifying new outbreaks for targeted interventions. In countries where case numbers remain high (like the UK), genome sequencing serves as a backup when contact-tracing efforts fail. Research shows that outbreaks are shorter and smaller when genome sequencing is used to support contact-tracing efforts.

The capacity for sequencing Covid-19 varies widely from country to country. In March, the UK allocated £20 million to launch the Covid-19 Genomics UK Consortium (COG-UK), an initiative to increase the country’s capacity to sequence Covid-19 genomes from a network of 12 sequencing centres, with the results informing the development of drugs, vaccines and other responses. After six months, COG-UK had already sequenced over 61,000 samples (equivalent to 15% of cases). In comparison, the 2014-16 west Africa Ebola epidemic resulted in the sequencing of 1,610 samples – only 5% of all infected cases over three years.

The inequality in sequencing capacity and the need for decentralisation to regions in the global south is clear. A mere 2 per cent of the 95,000 sequenced Covid-19 samples on the global database come from sub-Saharan Africa. In the region, Democratic Repulic of Congo has contributed the second-most genome sequences, with the reason for this speculated to be the legacy of foreign interventions from previous Ebola virus outbreaks. Nigeria’s Centre of Excellence for Genomics of Infectious Diseases was the first on the continent to sequence Covid-19, yet its ability to ramp up sequencing has been limited in the continent’s largest country with a Covid-19 caseload of nearly 55,000

Effective government response and vaccine development suitable for the continent will be enhanced by decentralising genomic sequencing of disease-causing pathogens in sub-Saharan Africa. The lack of genome sequencing is considered a primary reason why the vaccine for Rotavirus, a common disease among children globally, was effective in Europe and North America, but not in sub-Saharan Africa. The distasteful comments from researchers in Paris regarding vaccine trials in Africa reminded us of the importance of local ownership and building the capacity of governments to lead the Covid-19 response and corresponding research. 

The MRC Unit The Gambia at LSHTM is looking to replicate its successful efforts in building the Government of The Gambia’s capacity for molecular testing of Covid-19 with capacity building for genome sequencing. The genomics team at the Unit is leading the sequencing of confirmed Covid-19 samples in the country and the team has capacity to sequence hundreds of samples per week using small portable sequencers.

Governments and the international community should invest in decentralising genomics capacity to better inform vaccine development and Covid-19 response efforts. Most molecular diagnostic labs with capacity for Covid-19 detection can sequence Covid-19 samples with the estimated cost of acquiring sequencing instruments and reagents around £21,000 per lab (about £76 per sequenced sample). As a lighter touch option, a regional approach can target investments towards molecular labs with pre-existing sequencing capacity to scale up operations and develop logistic corridors across borders.

At the beginning of the Covid-19 pandemic, governments across sub-Saharan Africa demonstrated a tremendous willingness and ability to undertake testing. Countries like Ghana, Kenya and South Africa maintained open public-testing policies. Rwanda and Uganda managed to grow testing capacity exponentially, to keep pace with the virus and give confidence that control had been attained. Investing in genome sequencing offers an opportunity for governments to demonstrate their short-term commitment to an informed response and the long-term commitment towards contributing to vaccine development. The international community should stand alongside governments in sub-Saharan Africa to decentralise the technical capacity for genome sequencing.

Appendix

Figure 1: Mapping the first 35 Covid-19 cases in The Gambia 

Flow diagram

View full screen

Figure 2: Genome sequencing of Covid-19 samples in sub-Saharan Africa

chart of Genome Sequencing of COVID-19 Samples in sub-Saharan Africa

Figure 3: Budget for equipment to upgrade molecular lab for genome sequencing

Budget for Genome Sequencing Covid-19 Samples

Item

Cost

No. of reactions

Per sample cost

Hardware - Fixed Cost

 

 

 

PCR workstation

£1,000

   

Qubit fluorometer or Nanodrop

£1,000

   

Ice bucket

£200

   

Pipettes and tips

£800

   

PCR machine

£4,000

   

Vortex

£300

   

Centrifuge

£400

   

Gel electrophoresis system

£5,000

   

Nanopore MinION

£820

   

Magnet for purification

£500

   

Sub-Total of Hardware

£14,020

   

Consumables

 

 

 

Nanopore flowcells (50/flowcell (1700X))

£500

50

£10.00

Nanopore library prep kit (S0X-LSK109)

£465

24

£19.38

Native barcodes (1-24)

£470

96

£4.90

NEB companion module

£712

24

£29.67

Artic primers

£2,115

2000

£1.06

cDNA conversion reagents

£1,894

200

£9.47

Multiplex PCR reagents

£292

500

£0.58

Magnetic beads

£896

1000

£0.90

Qubit reagents

£250

500

£0.50

Loading dye and red safe

£200

1000

£0.20

Sub-Total of Consumables

£7,793

   

Cumulative Total

£21,813

 

76.64

Total excluding items that might be available

£9,913

   

Note: Estimates from Dr. Abdul Karim Sesay, Head of Genomics Core Facility, at MRC Unit The Gambia at LSHTM

 

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