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Sequencing SARS-CoV-2 in Zimbabwe

By Teresa Street, Senior Research Scientist

The Team


In October 2023 I travelled to Harare, in Zimbabwe, to teach a team of scientists how to genome sequence SARS-CoV-2 using Oxford Nanopore Technologies sequencing. The team were taking part in a study to observe COVID infections in Zimbabwe and had a collection of over 600 samples they were keen to sequence.

I spent a week at Professor Tariro Makadzange’s Infectious Diseases Research Laboratory (part of the Charles River Medical Group), teaching the team how to prepare samples and analyse data using the Global Pathogen Analysis Service (GPAS).

Hard at work preparing samples for sequencing
Celebrating starting the first SARS-CoV-2 sequencing run

I’m so grateful I got to experience scientific research outside the UK, and I couldn’t have spent the week with a friendlier, more welcoming group of people. My time in Harare also really made me appreciate the facilities we have and the things we take for granted. We don’t have thunder and lightning storms so powerful they regularly knock out our power for hours at a time; nor do we have labs that leak under the sheer volume of rain that falls. We also take our superfast Wi-Fi for granted: trying to download software and upload data at 2Mb/sec is frustrating, to say the least!

The lab (in what used to be a peanut butter factory!)

This collaboration would have seriously struggled to achieve all it did in such a short space of time without the help of Bede Constantinides. He made himself available from back home for the whole week to hold our hands through setting up the computing and guiding us through the analysis, so that I could leave the team fully self-sufficient for all their future work.

I’m pleased to report the team have now finished sequencing their 600+ sample collection and are now using ONT sequencing for other studies.

Zimbabwe is an incredible country with fantastic people, and I really hope I have the opportunity to visit again one day!

Imire Lodge Rhino and Wildlife Conservation Reserve
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Infection Inspection in New Scientist!

You can read all about our latest Zooniverse project, InfectionInspection, in New Scientist (15 March 2023 issue).

This citizen science project is part of a larger project developing a new way of diagnosing infections resistant to antibiotics and brings together researchers from Medical Sciences, Physics and Oxford University Hospitals NHS Trust and is funded by the Oxford Martin School.

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Visual Paper

Ten Years of Population-Level Genomic Escherichia coli and Klebsiella pneumoniae Serotype Surveillance Informs Vaccine Development for Invasive Infections
 
https://pubmed.ncbi.nlm.nih.gov/33411882/
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Science Together in Oxford

Science Together is a series of workshops and events being held at the Oxford Museum of Natural History on Tue 7 June 2022. Events start at 10.30am and run until 5pm.

From 5-7pm you can find out more about some of the projects through Science on the Sofa where Oli Moore will talk to some of scientists behind the different public engagement projects on display during the day, including our very own Carla Wright and Emma Pritchard!

You can register to attend in person, or follow the livestream, via this link.

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BashTheBug on the Zooniverse News

BashTheBug paper out!

Read the first scientific paper published in eLife. Anyone can go to the website and read it, there is no paywall.

Each image is looked at by up to 17 different citizen scientists — in this paper we show that taking the median of these classifications is both reproducible and accurate.

In fact, if you apply the criteria defined by the relevant ISO standard their results are sufficient accurate but not quite reproducible enough to qualify as an Antibiotic Susceptibility Testing device.

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Listen to Sarah Walker talk about the ONS Covid population survey

Professor Sarah Walker has been Principal Investigator of the ONS Covid Infection Survey since it started in April 2020. By regularly testing random samples of the UK population for infection and Covid antibodies, this has provided hugely valuable information as the Covid pandemic has progressed and has helped inform public health policy.

You can listen to her talk about the survey in the first episode of the new Statistically Speaking podcast by the Office of National Statistics (ONS), along with other people heavily involved in the survey.

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Listen to Tim Peto talk about LFTs

Listen to Professor Tim Peto be interviewed on Radio 4’s PM programme about the UK validation of SARS-CoV-2 lateral flow tests. You’ll need to go to about 15 minutes in to hear the start of the piece.

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News Tuberculosis

Read about tuberculosis and CRyPTIC in the Economist

Hot on the heels of the press release, the Economist have published an article describing the work of the CRyPTIC project.

Note that it is behind a pay wall, but you can always buy a copy of the print edition when it comes out on Friday 23 October 2021!

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News Tuberculosis

Derrick Crook interviewed on the BBC World Service

You can hear the CRyPTIC Principal Investigator, Prof Derrick Crook, talking about the project and its impact on tuberculosis on News Hour on the BBC World Service here. The segment starts about 35 minutes in. You will need a BBC login so this link may not work for everyone.