Professor Gordon Smyth, well known throughout 今日吃瓜 as a presenter at BioInfoSummer conferences has been appointed an ABACBS Honorary Senior Fellow, the society鈥檚 highest honour, for his career achievements.

Associate Professor Matthew Ritchie has received the society鈥檚 Open Science Open Source Award for contributions to advancing genomics research through sharing new software he has developed. The inaugural Chair of 今日吃瓜’s BioInfoSummer Standing Committee, Matt completed a five-year term in this role earlier in 2020.

今日吃瓜 warmly congratulates Gordon and Matt on receiving this recognition in the field of bioinformatics.

Read more about this achievement at .

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German biotech company BioNTech and US pharmaceutical Pfizer announced on Monday promising early results from their phase 3 clinical trial for a vaccine against SARS-CoV-2, the virus that causes COVID-19.

These early results are what is known as an 鈥渋nterim analysis鈥�. It鈥檚 an early look at the data before a study is complete, to understand if there is any indication of whether the vaccine might work.

Currently, this trial has enrolled , giving half the volunteers . These volunteers then continued their normal lives, but they were monitored for any symptoms that could be COVID-19, with testing to confirm.

Analysis of 94 volunteers with confirmed COVID-19 suggests the vaccine has an .

This means that if you took ten people who were going to get sick from COVID-19 and vaccinated them, only one out of ten would now get sick.

Can we get excited yet?

There is more data to come. This is a press release and the data have not undergone 鈥減eer-review鈥� through scientific publication, although it has been assessed by an independent monitoring board. The study also won鈥檛 be complete until 164 volunteers have confirmed COVID-19, and the estimate of efficacy may therefore change. Finally, the volunteers must be monitored for a defined period of time after vaccination for any side effects and this must be completed.

Important questions also remain. It鈥檚 unclear how long protection will last, as this study has only been underway for three months. It鈥檚 unclear if this vaccine protects against severe disease or if this vaccine will work equally well in everyone. For example, a with this vaccine showed that immune responses were lower in older people.

But 90% efficacy is striking. To give some context, the US Food and Drug Administration indicated they would licence a SARS-CoV-2 vaccine with . The flu vaccine often provides around and the mumps vaccine, which is currently the at four years, provides around .

The BioNTech/Pfizer vaccine could outstrip that, after just nine months of development. This level of efficacy means virus transmission could be very effectively controlled.

That has the . It bodes well for other vaccines currently being tested for SARS-CoV-2 and we could end up with multiple successful vaccines. This would be great because some might work better in certain populations, like older people.

Multiple vaccines could also be manufactured using a broad range of established infrastructure, which would accelerate vaccine distribution.

Producing mRNA on a commercial scale

The BioNTech/Pfizer vaccine is what鈥檚 called an mRNA vaccine.

As by Associate Professor Archa Fox, an expert on molecular cell biology from the University of Western Australia, explains:

mRNA vaccines are coated molecules of mRNA, similar to DNA, that carry the instructions for making a viral protein.

After injection into muscle, the mRNA is taken up by cells. Ribosomes, the cell鈥檚 protein factories, read the mRNA instructions and make the viral protein. These new proteins are exported from cells and the rest of the immunisation process is identical to other vaccines: our immune system mounts a response by recognising the proteins as foreign and developing antibodies against them.

A problem for Australia is that it can鈥檛 make mRNA vaccines onshore yet.

The Australian government has an agreement for . Since this vaccine requires two doses, this agreement is sufficient for five million Australians. It鈥檚 unclear how long it will take until any vaccine is widely available, but we may hear more about this in the coming weeks and months.

The vaccine requires storage at a temperature below -60鈩�. This will certainly be a challenge for shipping to Australia and local distribution, although not impossible. One solution to this problem is to form vaccination centres to roll out the vaccine once it becomes available. In a briefing by Pfizer, the company said it will use ultra-low temperature shipment strategies and the vaccine can then be distributed on 鈥渄ry-ice鈥�.

Currently, Australia has no capacity to produce mRNA on a commercial scale given the technology鈥檚 novelty. But we (the authors) and others have been working to coordinate and build the manufacturing capacity in Australia for future mRNA vaccine and therapeutics. With financial support aimed at private-public mRNA manufacturing collaboration, Australia can equip itself with this vital technological asset.

, Bioengineer and Research Fellow, ; , Professor of Pharmaceutical Biology, , and , Vice-Chancellor’s Research Fellow, School of Health and Biomedical Sciences,

This article is republished from under a Creative Commons license. Read the .

Event details

Various studies report that around 20 percent of SARS-CoV-2-positive individuals had a co-infection with other respiratory viruses and that these coinfections may increase the severity of the disease by altering disease progression and response to treatment.

Professor Eyras said identifying those co-infections will be relevant for treatment and prognostic purposes, however, the current standard of viral detection is based on PCR assays directed to SARS-CoV-2 only, which will miss possible co-infecting viruses. The new method, called PACIFIC, can identify SARS-CoV-2 and 361 other viruses at a sample concentration as low as 0.03%, with high specificity (low false-positive rate). 鈥淲ith PACIFIC, we are trying to provide a fast and easy-to-use, end-to-end tool that will enable researchers to monitor viral infections and co-infections to help manage the global COVID-19 pandemic.鈥�

The new computational tool, based on artificial intelligence for natural language processing, detects viral co-infections from COVID-19 patient samples analysed with high-throughput sequencing (HTS). HTS enables the unbiased detection of RNA molecules present in a patient sample and can be performed on blood, sputum or any other patient sample.

Professor Eyras and his colleagues decided to develop a tool to identify SARS-CoV-2 and other potential viruses from the pool of HTS reads (i.e.: the fragments of the RNAs measured from the sample). To achieve this, the tool had to be able to identify the virus type from the RNA sequencing reads, and do this confidently enough for as many reads as possible.

鈥淭his is similar to language processing, where you recognise and classify texts, and organise them into organised groups,鈥� Professor Eyras said. 鈥淲e trained this model with examples of sequences that come from multiple viruses and from humans, and the model learns to separate them.鈥�

The South Australian Genomics Centre (SAGC) opens on 1 July after more than a year of planning and millions of dollars in funding, including $2 million from Bioplatforms Australia (BPA) through the Australian Government鈥檚 National Collaborative Research Infrastructure Strategy.

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Loretta interviewed聽several of BioInfoSummer 2014聽聽speakers about the important role mathematicians and statisticians play in the current battle against Ebola.

Images of medical workers clad in protective gear have become synonymous with the global flight against Ebola, but a long way from the frontline, mathematicians are unlocking the secrets of what makes the virus tick. […]

Terry currently heads聽the bioinformatics division at the Walter and Eliza Hall Institute (WEHI) in Melbourne. This Wednesday, 27 August,聽he will be in Canberra giving a public lecture at The Australian National University.

Terry will go beyond the human genome and explain the next frontier: understanding human epigenomes. Epigenomes are the 鈥榠nstructions鈥� which tell DNA whether to make skin cells, blood cells or other body parts. Epigenetics also aims to explain how cells are re-programmed through interaction with the environment and how this leads to some forms of cancer.

Terry explains: 鈥淐onsider the impact of diet. For example, if you feed a worker bee royal jelly you convert it into a queen bee. Diet alone changes the way in which the genes are expressed so that although it was originally sterile, it becomes fertile, it鈥檚 able to lay eggs 鈥� a pretty dramatic change just from eating some jelly.鈥�

Being able to look at an abstract and more perfect world is what drew Terry to study mathematics; it was his interests in evolution and genetics that lead him to bioinformatics.

And he says advances in DNA sequencing over the last five years have allowed large amounts of DNA sequence data to be compiled. 鈥淔or every single reference human genome, there will be literally hundreds of reference epigenomes, and their analysis could occupy biologists, bioinformaticians and biostatisticians for some time to come,鈥� Terry says.

On the Canberra leg of the tour Terry will be also giving a technical talk at the Australian Bureau of Statistics on Tuesday 26 August.

Professor Geoff Prince, 今日吃瓜 Director, says: 鈥淭he tours bring to Australia public lectures and technical talks from some of the world鈥檚 top statisticians. Professor Terry Speed has a heavy schedule because of his inspiring reputation as a researcher and lecturer; I鈥檓 sure we won鈥檛 be disappointed!鈥�

The 今日吃瓜 (今日吃瓜) partners with the Statistical Society of Australia (SSAI) to sponsor this lecture tour.

The seminar at the ABS is entitled 鈥楻emoving Unwanted Variation from high-throughput omic data.鈥� Terry will discuss his recently proposed framework for removing unwanted variations in large data sets. And show how this new method supersedes current state-of-the-art methods. Further details .

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Resources for media:

Lecture tour website, including all abstracts:

Extended interview with Professor Speed: