Grant Jacobs

Dr Grant Jacobs is a computational biologist, a biologist who uses computers (algorithms, statistics, etc.) to explore biological systems, and who develops computer algorithms and tools for biologists to explore data from genes, genomes and proteins. He contracts to research groups and biotech companies through his Dunedin-based consultancy, BioinfoTools. He has an established interest in science communications and is open to science communication work as well as computational biology. Grant is on Twitter, @BioinfoTools.

COVID-19 vaccines prevent spread of the virus too - Code for life

May 13, 2021

Many people seem to be reading that our COVID-19 vaccine won’t prevent the spread of COVID-19 from one person to the next.1 If you’re worried about this, this one is for you. We now have evidence the vaccine reduces transmission, and a rough idea of by how much.2 Science is often about pulling different pieces of evidence together, in this case two large studies from the UK. The ONS study shows one dose of vaccine reduces the chance of getting an infection from someone else to about one-third (1/3) of that of unvaccinated people. (The vaccine also reduces the severity of those infections. Very few fully vaccinated people need hospital care.) The PHE study shows vaccinated people who become infected were about one-half (1/2) less likely to infect others in their household compared to unvaccinated people. Taken together, vaccinated people … Read More

Blood clots, vaccines and the need for baselines - Code for life

Mar 15, 2021

Some nations are pausing their AstraZeneca COVID-19 vaccine campaigns over concerns that it may be linked to blood clots. International media is is reporting it widely. I’m seeing concerned people asking questions on social media. Evidence so far indicates this is unlikely to be a real issue, but one that is being checked out of caution. One thing it illustrates is how helpful it is to have baseline data when rolling out major health efforts like these vaccination campaigns. Baseline statistics can head off potential ‘scares’ by telling us what are real concerns, and what are not. If after a treatment the same or fewer people have the ill-health event as those without the treatment, it’s unlikely the treatment is causing it. In New Zealand, a research group lead by Helen Petousis-Harris is working on baseline data for NZ’s … Read More

B.1.1.7 variant – early result suggests longer infections, management questions - Code for life

Feb 21, 2021

Sometimes it’s smaller, intensive studies that shed light on issues. Just reported results of daily sampling of COVID-19 patients indicate patients with the B.1.1.7 variant first observed in Kent, UK may have a longer infection compared to patients infected with non-B.1.1.7 variants. This is the variant seen in NZ’s most recent outbreak in Auckland. If this observation bears out in further studies this may affect how we manage B.1.1.7 cases. Longer lag periods would signal more caution in identifying and shutting down outbreaks; longer infections (and likely a longer infectious period) suggest there may be a need to isolate these patients for longer. It’s a call for more data to check this out. The results are from a small sample—just seven B.1.1.7 cases—but may explain this variant’s tendency to be hard to put down. We know that B.1.1.7 has more … Read More

COVID-19: backing our front row - Code for life

Oct 23, 2020

New Zealand has been called out as an outstanding player in managing COVID-19. We’ve done well,[1] but we’re far from perfect. We could do a lot better at backing our front row. Epidemiologists advise nations not to play “wait and see”. If By the time they do see, it’s all over them. “She’ll be right”… until it isn’t. We’re less likely to have restrictions imposed if we all play our part. Like in team sports, it’s no good just watching someone attack. You’ve got to step up and defend. No good just watching your front line cover you either: everyone needs to be in the game. On the game It’s a crucial rugby test match. The All Blacks’ opposition are being held behind their goal line (the border). The opposition has the ball, and they’re not letting it go. It’s … Read More

COVID-19: sequence the viral genomes of all border cases - Code for life

Aug 17, 2020

New Zealand has an advantage in managing COVID-19: all our cases come from the border, one way or other.[1] We can exploit this in how we shut down outbreaks. One way is to have at the ready the viral genomes of all border cases. With this we can quickly find the starting point of any outbreaks inside the country. If the genome sequence of a case within the country very closely matches a case at the border, that’s likely where it started. Because our cases come from the border, viral genome sequences can be a shortcut to find the index case, a key to finding all people in an outbreak. To be in with a chance of finding a match this way, we need to collect all the viral genomes from positive cases at our borders we can. Joep de … Read More

Lifting our game against COVID-19 - Code for life

Mar 23, 2020

We need to be lifting our game against COVID-19. [Edit: this was written before to the announcement of the Level 4 lockdown, and the National State of Emergency. The explanation of why we’re doing this, and general points should still be useful.] You and I need to help those working to prevent the spread of COVID-19 while they’re trying to lift the testing and treatment efforts. We don’t want to be playing this game running backwards. Best to play it solidly forward, from the start. So, what you and I need to do, and why?[1] Don’t overwhelm critical care We do not want the health system overwhelmed. It all comes back to this. Forget that detailed stuff about case fatality rates, R0s, whatever. If the health system is overwhelmed everyone who needs that care is affected – not just people with COVID-19. And … Read More

Is 2019-nCov a pangolin coronavirus? - Code for life

Feb 08, 2020

Tonight’s news suggests the coronavirus outbreak may have originated from pangolins. Details are very sketchy, almost nothing at all beyond a claim of high similarity. My impression is this claim comes from a press release by South China Agricultural University. Initial discussion online suggests this is a more likely candidate for an intermediate host than previous speculations. It is also ‘science by press release’, where claims are made in advance of publication of preprints, research papers or data. Spiny anteaters Pangolins are also known as ‘spiny anteaters’, small mammals covered in scales that feed on ants and termites. They’re nocturnal, and roll themselves into defensive balls when provoked.[1] Are you in there, Mum? Pangolins are known to curl up into a ball in defence. I’m no pangolin biologist. Perhaps tired Mums also roll up when they want a … Read More

The 2019-nCov coronavirus outbreak: all together now - Code for life

Feb 01, 2020

There’s so much being reported about the ‘Wuhan’ 2019-nCov coronavirus outbreak it’s confusing. Here’s an outline of some aspects of what scientists are looking at, some places to follow the story, and a few tips for reading the science. Yesterday Tedros Ghebreyesus, the Director General of the World Health Organisation (WHO) wrote, calling for a public health emergency – I am declaring a public health emergency of international concern over the global outbreak of #2019nCoV, not because of what is happening in #China, but because of what is happening in other countries. Not (yet) a pandemic call The WHO International Health Regulations Emergency Committee is not calling 2019-nCov a pandemic.[1] Formally it is a ‘public health emergency of international concern’ (PHEIC). The aim is to assist countries that are less able to prevent entry and spread of the illness. For example, … Read More

The coronavirus outbreak: what is R0? - Code for life

Jan 29, 2020

There are a few misunderstandings about the coronavirus outbreak from Wuhan getting around. Below is a short explanation of one of them: what is R0, and what does it mean. Current estimates for R0 centre around the mid 2s—call it 2.5 or thereabouts—not the higher values some are scare-mongering online. In following posts I may explain other things—if there’s something you’d like covered, let me know. What is R0? R0 (R-naught) is the basic reproduction rate, how many other people one infected person typically infects. I’ve emphasised typically as it is an average of many different scenarios. R0 estimates also assume everyone is susceptible to the disease. You’ll often see these quoted as a single number. In practice a range of scenarios are played out in modelling, with a range of values for R0 estimated. The single figure … Read More

Whodunnit? Finding the mystery 1080 testing lab - Code for life

Dec 01, 2019

1080 is used to control pests in NZ. Its use is contested by a noisy few. A new report claims high levels of 1080 in rats washed up on a beach. Flora and Fauna of Aotearoa (F&F) won’t name the laboratory that did their testing. It has sparked a hunt for the mystery 1080 testing lab. It’s just the sort of thing my readers might spend some idle time on Sunday searching for clues. Whodunnit? Readers can tackle Farah Hancock’s and Dave Hansford’s coverage (published in that order), and the Science Media Centre’s Expert Reaction report for background. You can also read the report itself (PDF file; obtained from a link in the SMC Expert Reaction report). Let us know what you think! F&F spokeswoman Di Maxwell claimed to Dave Hansford their tester previously … Read More