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 Worried about getting your vaccine or want a simple explanation? - Code for life

Oct 16, 2021

Worried about getting your vaccine? Let me tell you a secret. No-one likes getting a vaccine. People do it because they know they’re better off to. Let me tell you another secret, a weird one: the vaccine doesn’t really “do” anything. Confusing? Let me explain… Vaccines are a face at the right place, at the right time. The vaccine isn’t doing anything, though. It’s not a drug doing some chemistry. It’s just standing there, letting your body take a snapshot of it. It you want a little more than ‘it works’, but without the really deep stuff; this is for you. What’s happening Scientists and doctors often talk about vaccines as if they were drugs, “the vaccine gives you protection from the virus”. It’s a shorthand for a long, clumsy explanation of what happens. All the work, the doing, is … Read More

COVID-19 Helping people check locations of interest - Code for life

Aug 27, 2021

OPINION. It’s important locate as many people who have been at locations of interest as possible in New Zealand’s Delta variant outbreak. Because few people have been scanning QR codes or keeping other personal records we’re relying on people to check the Ministry of Health’s list of locations of interest. A few initiatives might help this. People who’ve been at locations of interest are considered contacts. At the August 26th 1pm briefing we were told ~65% of contacts have been followed up, and 75% of these tested. In order to move to lower Alert levels, or end the outbreak, we need to have more coverage of these contacts. That’s not just about track and trace, but about people checking themselves. How can we help them get this done? An ‘intelligent’ table of locations that tracks user’s checking of the list … Read More

COVID-19 The rise and rise of Delta - Code for life

Jun 22, 2021

From media headlines it feels like hearing the boy cry “fire” in the theatre. There’s a new variant about. Or perhaps he is really a crier, calling out a new season of the show, a new plot twist with a craftier villain? The main feature in town is now the variant Delta—B.1.617.2—and its closest staging to us is a so far modest event in Sydney. Reviews from overseas suggests the new villain is crafty indeed. It’s a reminder the virus keeps evolving, and can keep evolving. The best way to avoid still-worse variants is shutting down outbreaks. There are hundreds of variants. Most mean little; a few are of real concern. Tracking systems identify ‘variants of concern’ (VOCs).1 Delta is one of them. With international air travel new variants are at any country’s doorstep. While our ‘open doors’ quarantine-free … Read More

Attempt to stop NZ vaccine rollout declined, government to pass new bill - Code for life

May 19, 2021

The High Court has declined an attempt to halt New Zealand’s vaccination rollout. It does asks the Crown to consider how their plans sit within current law. The government plans to pass a Bill under urgency today to tackle this. I think a fair question is if the deeper issue lies with a lack of mechanism for emergency use approval in New Zealand. (This is not a criticism of the court ruling: the judge is obliged to consider what is put before them, and rule on that.) The ruling A request for an interim order seeking to stop New Zealand’s vaccine rollout was brought to the High Court in Wellington by Nga Kaitiaki Tuku Ihu Medical Action Society Incorporated (KTI). This was declined — (Ultra vires means ‘beyond ones legal power or authority’.) Basically, the court declined the attempt to stop … Read More

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