Rapid in-country sequencing technology

23Nov 2020
Gerald Kitabu
The Guardian
Rapid in-country sequencing technology

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries.

The Presidential medal award winner who heads TARI-Selian in Arusha, Professor Joseph Ndunguru (C), leads scientists from various institutions in the portable genomics practical training using Oxford Nanopore technologies at the Nelson Mandela African Institution of Science and Technology (NM-AIST) in Arusha. Photo by Gerald Kitabu

Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable.

With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical.

Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts.

However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges.

Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology.

This workflow was used in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome.

This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time.

Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance.

Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories.

More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

Scientists from various institutions in Tanzania have advised the government, relevant institutions and other stakeholders in the country to invest in the Oxford Nanopare sequencing technology so that the technology can enhance socio-economic development of the nation.

The Oxford Nanopore sequencing is a unique, novel and portable molecular technique that enables direct, realtime analysis of long DNA or RNA fragments.

They said the latest technology which is used to sequence the genome of organisms such as animals, insects and plants, required adequate budget for development, promotion and training programs of young scientists so that they can carry out fruitful research, generate data, analyse them and make decisions right here in Tanzania without sending the samples overseas.

Speaking at portable genomics practical training using Oxford Nanopore technologies at the Nelson Mandela African Institution of Science and Technology in Arusha, they said with the technology in place, the scientists will be able to answer different research questions and solve farmers and other society problems on site in a very quick manner.

In the past, to get this useful research information, one had to take sample abroad and take many months to get back the results, but with this portable technology in place, one can get the results right away on site.

The training attracted different research institutions such as Tanzania Agriculture Research Institute (TARI), Tanzania National Parks (TANAPA), and the Nelson Mandela African Institution of Science and Technology (NM-AIST).

Prof. Joseph Ndunguru from Selian Agriculture Research Institute (TARI-Selian centre) said that if the portable genome sequence is easily made available can help to transform lives in all spheres of life and enhance socio-economic development in the country.

Professor Joseph Ndunguru (PhD), a Presidential medal award winner and one of the great scientists in Africa said there is a need for investment in this technology.

This technology can be used to analyse the DNA for animals, plant, insects, crops and many other problems on the spot without ending the samples abroad, he clarified. “Like here, we have analysed the DNA for the Giraffe, Cotton samples also insects like the whiteflies.

When you are sequencing the whiteflies, remember they are transmitters or vectors of viral diseases. So, it makes it easier to find out the viruses which are carried out by the whiteflies,” he said. room such as lab. It can solve the problem on site.

Citing an example, Nakei who is doing her PhD in Life Science, specializing in sustainable Agriculture at Nelson Mandela explained further that if there is an outbreak of pests, there is no need to take the samples to the laboratory, what one need is to do it right on site.

“With this technology, a scientist or a researcher does not need to take the samples to the laboratory, extract the DNA and send them overseas for sequencing, instead he or her will just do it in the field.

This also allows the scientist to have data bank of line that he will need to download the data from gene bank or from the local data and then when he goes to the field, it will be much easier for him to get the solution on the problem.

“It is much easier to get the solution. He or he can extract the DNA, sequence, analyse the data and get the results. It is a very good technology for smallholder farmer in Tanzania and sub-saharan Africa,” she said.

I advice that the technology should be adopted countrywide, in the higher learning institutions and research institutions to help the farmers solve problems for their crop, wildlife and many other fields.

Computational Biologist, Laura Boykin who is based in USA said with portable genomics using Oxford Nanopore technologies, there will be no more sending samples overseas, and no more wondering what kills something.

“Just taking technology into the hand of people and transforming lives. Here, I mean development of science and technology has become so powerful. The biggest thing we can do is to train young students, raise awareness around this technology,” she said. Our main mission is sustainability in the sense that we don’t needs always overseas funders always coming to fund.

We real want the local government to support this work and empower the young scientists to be able to generate data in Tanzania, keep the data here and make decisions here in Tanzania, he said.

‘I would like to advice the local government to shift powers from samples going overseas and sometimes data coming back. It is high time the government supported this portable genomics Nanopore technology and empowered the scientists to be able to generate data, analyse them and make decisions right here in Tanzania.

This portable device can also be used to genotype plant and animal species in the National Parks. The information can be generated by the technology and that information can be used to understand genetic biodiversity in the national parks for effective and efficiency management and conservation.

The technology can tell which species are endemic, endangered and which species are invasive. The technology can also tell where the invasive species came from and when, what changes have taken place from time to time since they landed and invaded that particular area.

“In the past, to get this useful information, one had to take sample abroad and take many months to get the results but with this portable technology, one can get the results right away on site,” he said.

Explaining the objective of the training, one of the training facilitators, Charles Kayuki said the aim of the training is to equip scientists and researchers working on genomic studies so that they can have access to portable, affordable and widely used portable Oxfoford sequencer in their labs.

“When this objective is achieved, it means that when there is an outbreak of diseases for example in our environment, it is very difficult to know the causative of the outbreak. Therefore, it is this sequencing technology that will help the farmers and scientists to understand the exact cause of that problem on time,” he said.

Therefore, if the country manage to equip the scientists , it will help them much to respond to different problems in a very quick and timely manner, he added.

Advising the decision and policy makers, Kayuki said that usually scientists work under a chain of command, they can have knowledge on a certain technology but they cannot do it on their own so, we usually need assistance from policy and decision makers for support.

So, my advice to both members and those who can help scientists to move forward is to give these scientists a sort of funds that can work and deliver results that can real change the Society.

TARI Kihinga centre Director Dr. Filson Kagimbo explained that the technology has come at the right time. It should be supported by both decision and policy makers. It can be used to sequence genome of organisms such as animals, pest and plants on time without wasting much time to take the samples abroad.

“My centre has the mandate of coordinating oil palm research in Tanzania, so, I have found this technology very useful for oil palm research in Tanzania because Oil palm is the new research area in the country. It just started in 2018.

Therefore, there is still a lot to do on Oil palm research. Explaining how the technology will help her studies, Monica Nakei from Nelson Mandela African Institution of Science and Technology in Arusha said the technology has simple techniques of extracting DNA and does not need a specialized

room such as lab. It can solve the problem on site. Citing an example, Nakei who is doing her PhD in Life Science, specializing in sustainable Agriculture at Nelson Mandela explained further that if there is an outbreak of pests, there is no need to take the samples to the laboratory, what one need is to do it right on site.

“With this technology, a scientist or a researcher does not need to take the samples to the laboratory, extract the DNA and send them overseas for sequencing, instead he or her will just do it in the field. This also allows the scientist to have data bank of line that he will need to download the data from gene bank or from the local data and then when he goes to the field, it will be much easier for him to get the solution on the problem.

“It is much easier to get the solution. He or he can extract the DNA, sequence, analyse the data and get the results. It is a very good technology for smallholder farmer in Tanzania and sub-saharan Africa,” she said.

I advice that the technology should be adopted countrywide, in the higher learning institutions and research institutions to help the farmers solve problems for their crop, wildlife and many other fields.

Computational Biologist, Laura Boykin who is based in USA said with portable genomics using Oxford Nanopore technologies, there will be no more sending samples overseas, and no more wondering what kills something.

“just taking technology into the hand of people and transforming lives. Here, I mean development of science and technology has become so powerful. The biggest thing we can do is to train young students, raise awareness around this technology,” she said.

Our main mission is sustainability in the sense that we don’t needs always overseas funders always coming to fund. We real want the local government to support this work and empower the young scientists to be able to generate data in Tanzania, keep the data here and make decisions here in Tanzania, he said.

‘I would like to advice the local government to shift powers from samples going overseas and sometimes data coming back. It is high time the government supported this portable genomics Nanopore technology and empowered the scientists to be able to generate data, analyse them and make decisions right here in Tanzania.