A message to the TReND community

Dear TReND in Africa community!

We hope that you are all well. We have seen with horror how Covid-19 is ravaging European countries with good health infrastructures, such as Spain or Italy, and even in the UK, the situation is difficult. As we see the news of how the virus has by now reached most African countries, we wanted to encourage you as academics to play a central role in the local management of this epidemic. Here are some of the things that you can do. This advice is based on what we have seen work or not in Europe and is not comprehensive, but we thought that if we all get together in our respective countries, we might be able to make a big difference in people’s lives.

1 – Please, now more than ever, it is essential that you engage in outreach. We would like to ask all of you to explain to people how the virus works, and how everyone can do their part to protect themselves and others. Here are some key points that you could explain the general population:

The virus enters the body mostly through your mouth, nose, and eyes. This is why it is so important to not touch your face while on the street and to wash your hands
The virus is covered in a layer of fat if that layer is destroyed then the virus dies. Soap destroys fat, therefore is the best weapon we have against the spread of the virus. This is why washing hands regularly with soapy water is so important. The virus can stay on surfaces for a very long time (it is not clear how long but could be days!), therefore it is important to wash surfaces, also food like vegetables bought in the market should be washed with soapy water before putting in the home. Because fat is also dissolved with heat, cooking food is another efficient way of destroying the virus. We found that explaining things in these simple terms to the general public was very effective.
The virus is transmitted when people cough onto other people or surfaces that are touched by other people. Therefore, if you leave the house, try to not touch many surfaces and always wash your hands afterward. Because when people cough the virus can travel in the air up to 2 meters, it is important to keep a distance of at least 2 meters between you and anyone else when on the street. This is what the authorities here call social distancing.
The virus is not killed with antibiotics, in fact, there currently is no treatment (don’t trust things you may have seen in social media/news). If people develop symptoms such as fever and dry cough, the best thing they can do is to stay at home without close contact with anyone to not transmit the virus. If they are feeling seriously ill, they should be taken to the hospital with careful social distancing measures.
Most facial masks are effective if worn by the infected person to not transmit it to the rest. However, as a healthy individual, wearing a mask offers only limited protection. In particular, when you wear a mask you tend to touch your face more, increasing the risk of transmitting the virus from your hands to your eyes where it can enter your body. Therefore, masks can be efficient, but only if used correctly. It is important to explain this to people, so people who have access to or can build their own masks wear them but do so in the right way, and importantly don’t get a false sense of protection. You can still catch it even while wearing a mask.
In addition to conducting outreach activities, we encourage scientists to engage in dispelling misconceptions on social media platforms, by writing posts and making short videos. Most times, people download such videos and share them with other groups. This will help in debunking the disinformation going around on this new disease. We advise scientists to be guided by science supported by authorized institutions, such as the World Health Organisation, in the content they
produce.
We recently launched the African Science Literacy Network (ASLN) dedicated to promoting science awareness through scientists – journalists collaboration (www.AfricanSciLit.org [1]). ASLN has launched a COVID-19 dedicated page for articles and myth busters in English and different African languages (https://www.africanscilit.org/covid-19-updates). Get in touch with them if you wish to contribute articles in English or your local language to enhance awareness about COVID-19 during this trying time (info@africanscilit.org).
Finally, in the coming days, we will try to set up a google drive folder with resources for outreach for Covid.

2 – Early detection of cases followed by isolation is very important, in fact, it was deemed by the WHO as the best strategy to control the virus.
However, to detect positive cases, one needs to test. Now, testing is being a limiting factor everywhere. Here in the UK universities are trying to help the health system with this, but it is not easy. So we would like to ask you to be pro-active, please engage with your government and other institutions, every country needs to make use of all of its facilities and workforce to get enough testing going, but this needs to be prepared in advance. You possibly still have a few weeks before locally it gets as bad as it already is over here, but now is the time to engage in these conversations. There are some internationally approved tests, but these are expensive to run, there are not enough machines or reagents even in the UK to take on the required demand, and therefore people have started trying alternative
testing methods in research laboratories. When these are shown to work, we will try to convince our governments that several testing strategies need to be approved. Once they are approved, we gain capacity. This is the kind of discussion you need to engage in. Check the existing facilities and knowledge at your institution, inform yourselves, and engage with the government. Read up on and if you can try different diagnostic tests and evaluate which one is the best, then communicate this clearly to the government to get these officially approved for testing. Tens of thousands of the world’s top scientists in relevant fields are currently working together to find solutions, so the state of knowledge in this field changes daily. So keep up with the relevant literature, if you have the right expertise to digest them. You can find attached here a summary of the diagnostic tests that are out there with some explanation. Please read through these papers, forward this email to your colleagues. And again, by tomorrow we might already know more. Keep up to date.

Lastly, there is also a big effort from the open hardware community to help out, you can find a summary of these efforts in a paper we have recently written: https://www.preprints.org/manuscript/202003.0362/v1

It might seem that a single researcher cannot do anything, but together we can make a big difference. Ask yourselves, if not you, then who in your region can help?

Best wishes,

Lucia

In name of the TReND team.

A collection of useful links and information

This is a place to share protocols and information on Covid diagnostic methods and efforts at our institutions.

To join the OpenCOVID discussion:

https://join.slack.com/t/open-covid19/shared_invite/zt-cbji2hte-8jdoHpJDKg80ZliPVCIjqw (Slack Invitation)

https://app.slack.com/client/TUU48M0T1/C0103J8NF46/thread/C0102E5J2S3-1584911869.324700 (link to chlg-detect channel)

Overview

Tests basically fall into nucleic acid tests that detect viral RNA and reveal active infection and serological (antibody) tests that reveal well-established or prior infection. In general viral RNA tests will be more sensitive in the early stages of infection before antibodies have been generated. At present, viral RNA tests roughly divide into PCR tests which are typically the most sensitive and quantitative and other test strategies which are likely to be qualitative / less sensitive but may be simpler to run outside a laboratory setting.

PCR Tests

To do RT-qPCR but without RNA extraction

https://www.biorxiv.org/content/10.1101/2020.03.20.001008v1.full.pdf

To extract RNA without kit

http://www.en-journal.org/journal/view.html?uid=513&vmd=Full

Digital Droplet PCR for simpler quantification.

Alternative methods that do not use qPCR

These mostly come under the heading of isothermal amplification. NEB has pretty good coverage at their isothermal amplification page. In general these are likely to be qualitative rather than quantitative, less sensitive but simpler and faster to run and more compatible with point of care use. Some integrated procedures with one tube lysis/reaction look particularly interesting. The widely touted Abbott ID NOW test is of this class.

CRISPR based

https://www.broadinstitute.org/files/publications/special/COVID-19%20detection%20(updated).pdf SHERLOCK (Broad)

https://www.medrxiv.org/content/10.1101/2020.03.06.20032334v1.full.pdf DETECTR (UCSF/Mammoth)

A message regarding the COVID-19 pandemic

A message to the TReND community

A collection of useful links and information

To join the OpenCOVID discussion:

Overview

PCR Tests

To do RT-qPCR but without RNA extraction

To extract RNA without kit

Alternative methods that do not use qPCR

RT-LAMP

NEAR (Nicking and extension amplification reaction)

RPA (Recombinase Polymerase Amplification)

SENSR