By Grant Jacobs 22/06/2021


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 flights from affected areas in Melbourne were temporarily shut, they’re still open for people coming from Sydney.

Looking at the many locations of interest, and how other Australian states are blocking entry to people who have been at these locations, I imagine any further developments in Sydney will see this change. The Delta variant is also in another Pacific neighbour, Fiji.

There is no version of COVID-19 anyone “wants”, but the Delta variant is particularly concerning. What does it mean for us?

It –

  • spreads more easily, including among younger people
  • is about 40% more more infectious than Alpha, which is about 30% more infectious than original Wuhan strains2
  • seems to cause more varied and severe symptoms, with early symptoms more easily confused with a cold
  • it may affect younger people more than earlier variants

Overall, its more challenging in almost every way. That’s not to say limited, ‘narrow’, or confined infection chains can’t be managed, but that we need to be faster and firmer on this variant – and vaccinate.

A bigger nutshell

Delta gets about easier. Its more transmissible, and better at wriggling past a country’s COVID-19 defences. NZ’s easy complacency within the country leaves us vulnerable.

We’re lazy with our second-row effort. Too few people scan QR codes (turn Bluetooth on!). We rarely wear masks on public transport. We’re not keeping up our hygiene measures. Our buildings have poor ventilation—a very important factor, especially over winter when we’re indoors more. Fewer than 325,000 people in NZ have been fully vaccinated.3 The travel bubble with Australia increases the opportunity for cases, with more entry points into a larger population. There are concerns our track and trace capacity is limited,

Documents from the Auckland Regional Public Health Service (ARPHS), obtained by Stuff, showed that when the Valentine’s Day cluster was at its peak staff were struggling to contact trace just 160 people per day.

The Delta is on the rise in many countries worldwide. It’s been a dominant feature of the pandemic over the last few months. (More on this in the next section.)

Those surges aren’t just about the variant, but also reflect how each country is managing COVID-19 and how people behave. It’s hard to keep up the effort, but it’s important to. The more challenging variants test management approaches more strongly than earlier variants.

We’d like to be able to rely on trace and track for closing off incursions into NZ. Ultimately that relies on us—you and I—being more disciplined that we are right now.

If track and trace looks like being overwhelmed, we have take the hit and put restrictions in place. No-one really wants that.

Rising cases worldwide

The genome of the Delta variant was first sequenced in India,4 where it is a feature of India’s huge outbreak. It’s not “brand new”: it’s been around since late 2020 and is now found in more than 60 countries worldwide.5 Delta is likely to become dominant strain in many parts of the world just as Alpha (B.1.1.7) did.

Delta is replacing all other variants in the UK, and is rising in Scotland. Where the numbers of other variants fell during their lockdown along with the overall trend of falling case numbers, Delta rose against the grain. In the UK it now represents over 90% of variants sequenced.

They’re expecting a third ‘wave’ of infections, with particular concern about younger people. Cases are up 33% over the last 7 days; deaths up 23%. The UK are delaying their plans to open up.

The UK solution is vaccinate fast. They have excellent protection of those older than 60, with vaccination coverage in 90%+ range. They want to extend that record to younger people to prevent outbreaks from surging.

UK vaccination profile late June
(Source: 17th June report of NHS vaccination statistics.)

It’s on the rise elsewhere, too. Over 13% of newly sequenced SARS-CoV-2 virus genomes in the USA are Delta variants. There it’s one of two variants on the rise (Delta and Gamma).6

Nepal and Afghanistan are experiencing huge surges in cases, with limited hospital beds and oxygen supplies.

In Europe, a big rise in cases has closed travel in and out of Lisbon, a surge driven by the Delta variant. In Moscow, 89% of new cases are the Delta variant.

Prevalence of Delta variant, source Financial Times
(Source: Financial Times, Delta variant begins to spread, threatening EU’s Covid progress)

In well-vaccinated Israel there are two outbreaks in schools. Schools feature in the UK’s rising cases, too.

Warning signs after early success

Low levels of vaccination leave some countries heavily relying on border measures, track and trace capacity, and (heavy) restriction measures if these fail.

Singapore, Japan, Vietnam, and Taiwan (among others) all have in common low levels of vaccination, and recent outbreaks of COVID-19.

These countries have excellent track records in managing COVID-19 over the last year-plus.7

An over-arching pattern may be that the transmissibility of new variants leave little room for weaknesses in control measures.

The wall needed to protect against Delta needs to be higher and tighter-packed than for Alpha.

Two walls for Alpha and Delta variants
(Source: Eric Topol, Twitter.)

In principle, ‘perfect’ control measures would do the trick.

Viruses are completely inert outside our bodies; they’re only active within cells. Movement of viruses outside of our bodies is dictated by the environment and us. If we could manage the environment and us perfectly, we could hold viruses out.

In practice systems are imperfect. Mistakes happen, and there are always some chinks in large, complex systems.

We expect there to be some breakthrough cases, eventually. How we respond to those matters, not just how good border measures are.

These outbreaks in Asia are a warning that countries relying on borders measures ultimately need vaccines to back them up, especially as people become complacent.

One striking thing, though. Most people want the vaccine, but I don’t see the same urgency in driving the second-line defence strongly until the vaccine rollout is complete.

It’s odd, really, and it’s not good. You’d think that if people worry about the first, they’d be very keen on the second. Instead New Zealanders seem to love “othering”, that someone else will take care of it, be it the vaccine, the border, or shutting down chains of infection.

More infectious

Unimpeded, a small increase in infectiousness can go a long way.

Take an imaginary and over-simplified case where infections typically spread to, say, 3 people. Imagine a new variant emerges that typically spreads to 33% more people.

This doesn’t seem much at first, it’s “just” typically infecting 4 people rather than 3. But after two rounds of infection that’s 16 new infections v. 9 new infections from the old variant (4×4 v. 3×3). After three rounds that’s 64 v. 27. Four rounds: 256 cases v. 81 cases.

You see where this is going, right? If it runs, it’ll run much faster than the earlier variant once it gets going. 

You want to close it off fast. You’re in with a chance in the early stages, but you don’t want to let it go.

(Actual rates of increase depend on a lot of things, and determining ‘real’ transmission rates are not easy. You have to factor in all the other things that might be affecting transmission. Also, COVID-19 infections are episodic. Most don’t infect many, but a few do.)

The UK Public Health England (PHE) studies report secondary attack rates (SARs), how often an infection person goes on to infect others. The SAR for Delta is about 40-60% more than that for the Alpha variant.

One measure of transmissiblity is R, the typical number people one infected person infects. Above 1.0, cases rise. The UK are reporting R=1.44. Another real-world measure is the doubling rate, how many days for cases (or hospitalisations or deaths) to double. In the UK the doubling rate of cases is currently about 11 days.

Bear in mind the UK has fantastic vaccination of their over-65s. Their increases are mainly limited to younger people. Imperial College London’s REACT study found the highest incidence in 5-12 year-olds and 18-24 year-olds.

Not an increase in death rates

There’s an increase in the virus’ ability to spread, but the UK are not seeing an increase in death rates. In the UK this may reflect a mix that it’s early in the outbreak, the lag in time between cases and deaths, and the very high vaccination levels in their elderly.

Deaths are rising sharply in Uganda, where the delta variant is driving a big outbreak. (From Twitter.)

Even an increase ‘only’ in infectiousness an issue, I’m afraid. Imagine, for arguments sake, there is 1 death in a 1000 cases.

Now imagine if that death rate stays exactly the same, but we double how many people who are infected. With twice as many cases we also have twice as many deaths.

It’s a reason some epidemiologists worry more about a rise in transmissibility than a rise in death rates per se. The first is nasty alright, but the second ultimately can be more of a problem.

The solution is to stop outbreaks from running. For small outbreaks, control measures (e.g. wear masks on public transport and indoors) can help key chains of transmission narrow, rather than diverging out to many people, and hence make the outbreak easier to track and trace. That’s where you and I can help: scan those QR codes, turn Bluetooth on in the app, wear masks when we’re asked to.

Vaccines can also help.

Vaccines to the rescue

Both the BioNTech/Pfizer vaccine that we use in NZ, and the Oxford/AstraZeneca vaccine evoke strong immunity against the Delta variant if you take both doses. That immunity protects us very well from severe illness.

PHE report vaccine protection against Delta variant v severe infection
(Data from Stowe et al, preprint; graph by Jonathon Li. Higher bars are better.)

The immunity developed from vaccination very strongly protects us from serious cases of COVID-19, but a few minor cases still happen.

Even a single dose offers good protection against severe infection. Hospitalisations are rare in people with both doses of the Pfizer vaccine, and deaths very rare.

Results from earlier research finds protection against milder symptomatic cases of COVID-19 is quite a bit less with just the first vaccine dose.

PHE report vaccine protection v symptomatic infection for Delta variant
(Graph by Jonathon Li. Higher bars are better.)

Each dose pushes down the severity of infection typically seen, so that under full vaccination we rarely see serious cases.

Another way of looking at it is that vaccination reduces your risk to the same as someone much younger!

Slightly less but still great

We are slightly less protected against the Delta variant than to earlier variants when fully vaccinated (93% → 88%), but it’s not a concern—it’s still very good protection.

The increased transmissibility of Delta means you even more want to get the vaccine, and if most people get both shots, it’ll nullify the ability of the Delta variant to spread and cause problems.

There’s lots I could say about vaccination itself, but this article is about the Delta variant! (If you’re interested aspects of vaccination, feel free to suggest what you might be interested in, see About the author.)

Community immunity

Vaccination can reduce the risk of severe infections (and death) to individuals. That still leaves a small risk of milder infection. It’s not yet known if the risk of so-called long-COVID comes down too.

As a population we can drive the risk even lower if we all pull together. By preventing the spread of the virus, we effectively reduce our personal risk right down to near zero.

Not zero, but close.

I tackled this in an earlier article:

At some time we have to open our borders to travel from overseas travel without quarantine. When we do, some people coming in will have COVID-19.

We want to keep transmission to thin chains of cases we can easily track, trace and isolate.

Even with many people vaccinated, there still will be a few people passing it on, just (much) less often. It’s likely this transmission will typically be of smaller viral loads, causing less serious infections.

Note we’re not expecting there to be no transmission from person to person. What we’d like is that what transmission there is doesn’t go far, and is easy to close off.

We need everyone who is able to vaccinate to get their shot.

A small number of people have medical reasons they cannot be vaccinated. Their safety depends on us vaccinating so that any chains of infections are unlikely to get to them.

An important bit to add is that the protection offered to communities by vaccination is a continual scale—every bit helps.

There is a threshold where, at least in theory, outbreaks would die out of their own accord in the face of the level of vaccination a population has. In practice it’s all of the measures that get us there, and vaccination, while an important measure, is just one of them.

The Delta variant

The Delta variant is a collection of 13 mutations that together characterise the variant. Four of these mutations are in the spike protein. Scientists often refer to Delta using the PANGO name of the lineage, B.1.617.2.

It’s one of three related ‘families’ of variants: B.1.617.1, B.1.617.2, and B.1.617.3. The first is the Kappa variant—the variant in the Melbourne outbreak. The last is still relatively uncommon, and we don’t have a lot of data about it.

(In later articles we could delve into the molecular details of the variants, and what their differences are; see the section below, Looking forward. I see very little explanation of what is really behind all this in media outlets. It’s as if all viruses are black boxes with the names of Greek letters stuck on them!)

About the author

I’m a scientist (a computational molecular biologist) and writer. I’ve tracked this pandemic from early on by fortuitous accident. Most of 2019 I researched zoonoses for writing projects. As part of that I looked for examples of outbreaks. In the first half of December 2019, a ‘pneumonia of unknown cause’ in China caught my attention, and I’ve followed the science and specialist’s discussions closely since.

Viruses are molecular life at its minimal, fascinating for anyone whose work examines how molecules interact and make life happen.

If you want to ask questions, you’re welcome. You’re best to try via Twitter.

Article by Grant Jacobs, ©2021-.

Looking forward

If there is interest I can write more about the Delta variant, dig into just what exactly makes it different; what is this new Delta+ variant; the molecular biology of how Delta might be directly moving from cell to cell; and so on. Or any other molecular and genetic aspects of COVID-19. A topic I will try cover is the origin of COVID-19 as it’s close to my interests.

A lot of material has been removed to get this article out. Most of that relates to vaccination rather than the Delta variant. I may come back to this.

It’s lot of work digging into the science. I enjoy learning the details, but it can be a strain doing this much unpaid! (My small output doesn’t reflect well the effort I have put into keeping up with COVID-19 science.) Suggestions on that front are welcome.

Other articles in Code for life

COVID-19 vaccines prevent spread of the virus too

Lifting our game against COVID-19 (From March 2020. I spent nearly a week trying nail what I thought was ‘the’ essential problem—the thing that could put it in a nutshell—for the section, Running the ICU.)

The coronavirus outbreak: what is R0? (My first post on what was then 2019-nCov.)

1000 of these now (links to many things I’ve written, including those below.)

Sea stars and mosaics

Coiling bacterial DNA

Finding platypus venom

Kumara are transgenic

Map shows New Zealand with lowest death rate on earth in 1856, over 11 in 1000 dying

Footnotes

1. Good technical information about the variants are Public Health England’s (PHE) weekly variants of concern technical briefings and the World Health Organisation’s (WHO) Weekly epidemiological updates. NZ’s MedSafe put the Ministry of Health’s Covid Science & Insights team’s occasional updates on variants on their COVID-19 Science News page.

I prefer PHE reports for Delta, as they delve into details superbly. The WHO reports include an international coverage section.

2. Estimates are rarely single figures; usually a range (low to high), and vary using different techniques. Delta is around 30–100% more infectious than Alpha; Alpha is about 40–100% more infectious than original SARS-CoV-2 strains.

3. Some people complain our vaccination effort is slow. In reality its as fast as our supply. You can’t go faster than your supply! Few countries have been able to order large (some would say excessive) amounts early; most of the planet is worse off than us. One important point: the relevant statistic is the number fully vaccinated, compared to the full population, not ‘over 16’.

4. That is not the origin or source of the variant, just the place it was first sequenced. It may have emerged in another country, perhaps a country with little genome surveying. We just don’t know.

5. Of countries with sequencing data, and some say 80+. Not all countries have good (or any) genome sequencing. Pathogen genome sequencing in every nation is one thing needed for future pandemic preparedness, along with better testing.

6. Other reports say ~20%. The lower figure is closer to WHO’s figures, valid from a few days ago.

7. If another person claims “NZ is the best”, I’ll scream. It’s driven me crazy for over a year. Vietnam in particular was ahead of us, ditto Taiwan. And South Korea. Even little Sarawak, where I was living. In a very real sense they went straight to what we started after our lockdown: they held it out from the get-go.

Featured image

False colour image of,

Transmission electron micrograph of a SARS-CoV-2 virus particle (UK B.1.1.7 variant), isolated from a patient sample and cultivated in cell culture. The prominent projections (green) seen on the outside of the virus particle (yellow) are spike proteins. This fringe of proteins enables the virus to attach to and infect host cells and then replicate. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland.

Source: Wikimedia, CCA 2.0 Generic license. Author: NIAID.