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Archive for the ‘herd immunity’ Category

A coronavirus update: new variants

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Everyone wearing a mask in this Tokyo airport, but still there are lots of problems, and lots of travellers

So there’s much concern about new variants of the SARS-CoV2 virus, one from the UK, now known as the Kent variant, and one from South Africa. My main source of info on this will be the SGU podcast 809, from January 6.
The Kent strain is more infectious than the original, by 50-60%, though not more deadly. However its infectiousness is fast making it the more dominant strain. The South African variant, though, is causing most concern, as virologists are uncertain about its response to the vaccines now available. It has some of the same mutations that are in the Kent variant, making it also more infectious, but it also has mutations that allow it to evade antibodies targeting previous variants. This won’t make the variant immune to the vaccine, but it will make the vaccine less effective, though exactly how much less effective is the big question currently.
Another major concern is that this new variant can infect people who’ve already contracted and recovered from the virus. As Dr Steven Novella and others on the podcast argue (and this quote is ‘tidied up’ from direct speech):

This is the result of allowing a pandemic to simmer along over time. Mutations are inevitable, though different viruses mutate at different rates. SARS-CoV2 has error-correction mechanisms when it replicates, so that’s why it mutates more slowly. But if an infection in an individual, or an epidemic, lingers long enough, you’ll still get mutations. Part of the problem is that, with so many people infected, for so long, there are a great number of opportunities for new variants to arise. There are thousands of roughly equivalent variants, which are neutral or inconsequential in effect, but now we have two variants that are more mutated, and more consequential. They have a suite of mutations that seem to have developed much faster than the background mutation rate of the virus. It’s thought that this is because in individual patients who’d had the infection for months and were being treated during that time, the increased selective pressure on the virus may have caused this suite of mutations to be formed. This kind of mutation rate has been shown in the lab with respect to antibiotic resistance in bacteria. 

The point here for the future is to get to a level of herd immunity through vaccination. Considering that new strains arise regularly, as with the flu (and we don’t yet know how regularly this will happen with SARS-CoV-2), it may be that the vaccine will have to be tweaked regularly to cover these new strains. Time will tell, and of course we don’t yet know how effective the new vaccines will be against these current major variants. In fact we don’t know for sure how long the vaccines, or the antibodies they create, will be effective, regardless of these variants. But mRNA vaccines can apparently be produced, and tweaked, quite quickly, once the variant’s RNA is sequenced.

All of this tells us that the science is generally on top of this. The major problem is political, and social. Trying to get people to do the right thing, to wear a mask, physically distance, avoid large indoor gatherings and to get vaccinated when the vaccine becomes available. This is easier in some regions of the world than in others, and the problems ranges from distrust or ignorance of modern science, to conspiratorial thinking, to rights over responsibilities, to cultures of compliance and non-compliance. Humans are delightfully diverse, or just a mess, and the WHO warns us that this may not be ‘the big one’ in pandemic terms. The year 2021 will not see the end of all this – far from it. 

Stop press – a new variant has just been found in Japan in four travellers from Brazil, the Sydney Morning Herald reports. Twelve mutations have been identified, one of which is shared by the UK and South African strains, suggesting a higher infection rate. The travellers are in quarantine in Tokyo airport. Due to a steep rise in cases, a state of emergency has been declared for Tokyo and surrounding prefectures. And so it goes.


Written by stewart henderson

January 11, 2021 at 10:47 am

the science of Covid-19: possible treatments, herd immunity

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Australia is now 22nd in the list of total COVID-19 cases and dropping down. There are still of course new cases every day, but far fewer than many countries below us on the list. Experts are now talking about a flattening curve, but they also warn that the virus is ‘here to stay’. Here in South Australia, there were no fatalities when I last posted, but there have been three in the last couple of days. There are a large number of cases recently linked to our Barossa wine-growing region, a popular tourist destination.

So let me take a closer look at the SARS-CoV-2 virus. It’s a positive-sense single-stranded RNA virus. RNA is generally single-stranded in nature, though apparently can be double-stranded on occasion. The positive-sense term refers to the polarity, or sense, of the RNA. It’s also called ‘positive-strand’, facing 5’ to 3’, which means it acts as mRNA and can be translated into viral proteins in the host cell.

These types of virus are very common. They include common cold rhinoviruses as well as the SARS and MERS coronoviruses. SARS-CoV-2 is genetically similar to bat coronaviruses, causing virologists to believe that it was transmitted from bats to humans through an intermediate species such as a pangolin. The reproduction number of the virus (R0) is currently ranged from 1.4 to 3.9, in a scenario of no immunity and no preventive measures taken.

It has often been repeated that a vaccine will take 12-18 months, if not longer, to be safe, ready and effective. Science communicators such as the ABC’s Dr Norman Swann are telling us that stay-at-home orders may need to stay in place until that time, which is surely alarming economists and the business community. So, unsurprisingly, people are looking to short-cuts and desperate remedies. Perhaps the most publicised of these is the anti-malarial drug hydroxychloroquine, aggressively promoted by the US President. It turns out, also not surprisingly, that he has some financial interest in the French company that has branded the drug, according to the New York Times. There doesn’t appear to be any clear evidence on the benefits of the drug. Best reports speak of ‘mixed results’.

There are reports also of the benefits of blood plasma from people who have recovered from Covid-19. A small Chinese study involved 10 severely affected patients being given a few hundred millilitres of ‘convalescent plasma’ containing viral antibodies, and results were described as promising. The approach is being tried in the US, with the Red Cross and the American Association of Blood Banks seeking to recruit suitable ‘fully recovered’ donors.

As people continue to be alarmed and frustrated at the massive disruption to their working and social lives caused by Covid-19, some world leaders (e.g Boris Johnson and his chief science adviser Patrick Vallance, and Netherlands PM Mark Rutte) have come up with not-so-encouraging solutions, such as allowing the virus to run its course so that the population can build up herd immunity. This would actually be a disastrous policy in the case of a virus with a high (but not precisely known) fatality rate, involving millions of severe cases requiring intensive care treatment at any one time.

Herd immunity occurs when enough people have antibodies to the virus that it has nowhere to go. This can occur through the work of our immune systems or through antibodies created by effective vaccination. The former obviously comes at a much greater cost in terms of lives lost, in the case of a highly infectious (the R0 is now estimated – the data changes as I write – at between 2.0 and 2.5), high-fatality virus. Also, because Covid-19 is new, we don’t have sufficient data as yet about the degree of immunity it confers upon recovered patients, or whether it is able to mutate to any degree. Experts are generally counting on low or no mutation, but none of them see relying on herd immunity to be a humane solution to the problem. Suppression is the name of the game at the moment (even though it will reduce herd immunity). That’s to say, the R0 mentioned above (which might be higher) is the figure without the application of physical distancing or other containment measures. The R0 number, if it can be ascertained, gives an indication of the percentage of immunity required to ‘protect the herd’. An R0 number of 2 will require about 50% immunity. If the R0 number is 3, some 66% immunity will be required. Measles has a very high R0 of 12, requiring 90% immunity, which explains why anti-vaccination movements can imperil whole communities.

So it’s a trade-off. Physical distancing measures will reduce the possibility of herd immunity – the production of antibodies. Going back to business as usual will increase infection rates – ok for those who recover, not so much for those who don’t. The cost of the second option, most will agree, is just too great.


Bloomberg news interview: Dr Josh Sharfstein (video)

Written by stewart henderson

April 9, 2020 at 9:14 pm