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The Mutated Virus Is a Ticking Time Bomb | The Atlantic.

[DECEMBER 31, 2020]

There is much we don't know about the new COVID-19 variant -- but everything we know so far suggests a huge danger.

Medics assess a woman for Covid-19 symptoms before taking her to a hospital


[The Atlanctic] Editor’s Note: The Atlantic is making vital coverage of the coronavirus available to all readers. Find the collection here.

Zeynep Tufekci writes:

A new variant of the coronavirus is spreading across the globe. It was first identified in the United Kingdom, where it is rapidly spreading, and has been found in multiple countries. Viruses mutate all the time, often with no impact, but this one appears to be more transmissible than other variants—meaning it spreads more easily. Barely one day after officials announced that America’s first case of the variant had been found in the United States, in a Colorado man with no history of travel, an additional case was found in California.

There are still many unknowns, but much concern has focused on whether this new variant would throw off vaccine efficacy or cause more severe disease—with some degree of relief after an initial study indicated that it did not do either. And while we need more data to feel truly reassured, many scientists believe that this variant will not decrease vaccine efficacy much, if at all. Health officials have started emphasizing the lack of evidence for more severe disease.

All good and no cause for alarm, right? Wrong.

A more transmissible variant of COVID-19 is a potential catastrophe in and of itself. If anything, given the stage in the pandemic we are at, a more transmissible variant is in some ways much more dangerous than a more severe variant. That’s because higher transmissibility subjects us to a more contagious virus spreading with exponential growth, whereas the risk from increased severity would have increased in a linear manner, affecting only those infected.

Increased transmissibility can wreak havoc in a very, very short time—especially when we already have uncontrolled spread in much of the United States. The short-term implications of all this are significant, and worthy of attention, even as we await more clarity from data. In fact, we should act quickly especially as we await more clarity—lack of data and the threat of even faster exponential growth argue for more urgency of action. If and when more reassuring data come in, relaxing restrictions will be easier than undoing the damage done by not having reacted in time.

To understand the difference between exponential and linear risks, consider an example put forth by Adam Kucharski, a professor at the London School of Hygiene & Tropical Medicine who focuses on mathematical analyses of infectious-disease outbreaks. Kucharski compares a 50 percent increase in virus lethality to a 50 percent increase in virus transmissibility. Take a virus reproduction rate of about 1.1 and an infection fatality risk of 0.8 percent and imagine 10,000 active infections—a plausible scenario for many European cities, as Kucharski notes. As things stand, with those numbers, we’d expect 129 deaths in a month. If the fatality rate increased by 50 percent, that would lead to 193 deaths. In contrast, a 50 percent increase in transmissibility would lead to a whopping 978 deaths in just one month—assuming, in both scenarios, a six-day infection-generation time.

Transmissibility increases can quickly—very quickly—expand the baseline: Each new infected person potentially infects many more people. Severity increases affect only the infected person. That infection is certainly tragic, and this new variant’s lack of increase in severity or lethality thankfully means that the variant is not a bigger threat to the individual who may get infected. It is, however, a bigger threat to society because it can dramatically change the number of infected people. To put it another way, a small percentage of a very big number can easily be much, much bigger than a big percentage of a small number.

I dismissed the news initially because viruses mutate all the time and there have been too many baseless “mutant-ninja virus” doomsaying headlines this year. The exaggerated, clickbaity alarmism makes it harder to discern real threats from sensationalism. Given the constant reality of mutation, genomic variants should be considered innocent until proved guilty. Even an increase in the proportion of cases attributable to a particular variant is not definitive proof of an evolutionary advantage.

However, as data on the new variant roll in, there is cause for real concern. Trevor Bedford, a scientist at the Fred Hutchinson Cancer Research Center and a board member for the Covid Tracking Project at The Atlanticpoints out that infections from the new variant are increasing very rapidly among the population in the U.K. Bedford also notes that this new variant seems to have a higher secondary-attack rate—meaning the number of people subsequently infected by a known case—compared with “regular” COVID-19.  Finally, the new variant seems to result in higher viral loads (though this is harder to be sure about as viral loads can be affected by sampling bias and timing). As Kucharski told me, all of this does not rule out other explanations. This increased transmission could be due to chance or founder effects—meaning one variant just happened to get somewhere before the other variants and then got “lucky”; it was early, rather than more transmissible. It could be due to changed behavior among people—quarantine fatigue, less masking—leading to more rapid spread. However, given the current evidence, along with the specifics of the mutation, it’s getting harder to assume that those other explanations are more likely than the simple proposition that this is truly a more transmissible variant.

So how much more transmissible? We aren’t completely sure yet, but the initial estimates from the data suggest that this variant could be about 50 to 70 percent more transmissible than regular COVID-19. To make matters thornier, we aren’t yet exactly sure why it’s more transmissible, though reasonable theories are already being tested. This variant, now called B.1.1.7, has “an unusually large number of genetic changes, particularly in the spike protein,” which is how the virus gains entry into our cells. The new variant may be better at eluding our immune response and replicating, or be able to better bind to locations in our body more conducive to infecting others, but that is all speculative for the moment.

This uncertainty in understanding the variant’s exact mechanisms means that we don’t know if our existing tools—masks, distancing, and disinfecting—are as effective as they were compared with an identical scenario with the regular variant. To be clear: The variant is still a respiratory virus, so the basic tools will not change, and they will all continue to work. In fact, they have become more important, but we may need to be stricter—less time indoors, better masks, better ventilation, more disinfection of high-touch surfaces—to get the same bang for our protective buck. It may be a small difference, or not. We don’t know. We won’t know for a while.

Given that this new variant is already here in America, are we too late? No, but we are on our back foot. The United States does not have extensive genomic surveillance, or a rapid turnaround with what surveillance it has, so in some ways, we are flying without a map. We have some indications that the variant is—so far—probably relatively rare in the United States.

This could, of course, change extremely quickly, before we can even detect that change, but that highlights the importance of early action. In addition to the threat of exponential growth, we must remember that this pathogen is quite overdispersed—meaning some people seem to cause many infections, while many do not transmit it at all (though these ratios may change as well). Early on, there was a lot of hand-wringing about why some European cities were very badly hit while others were spared—spared only until later, it often turned out—despite similar policies. The answer could be just a bit of bad luck and a few weeks of delay: For exponential processes, small initial differences can mean gargantuan differences in the long run, and we are not helpless.

We can and should deploy whatever weapons we have in our arsenal, as soon as possible. If public-health officials can accelerate our ability to detect the new variant, they must. “You could imagine case-based interventions specifically targeting the early variant-transmission chains,” Bedford told me. “I wouldn’t expect to contain them, but I could imagine buying a week or two.”

A week or two may not seem like a lot, but combined with other aggressive public-health measures, we may actually gain a few additional weeks. Maybe all of that could delay this new variant’s widespread establishment until February or even March.

This moment is somewhat similar to America’s initial COVID-19 surge and shutdown in March. We need to once again talk about the importance of flattening the curve. We need to again preserve hospital capacity, so our fatality rate doesn’t increase. But this time around, we can be a lot more hopeful: We need to flatten the curve because delaying potential infections just a few weeks or a month can make a tremendous difference when highly effective vaccines are being rolled out.

We are in a race against time, and the virus appears to be gaining an unfortunate ability to sprint just as we get closer to the finish line. Although the initial rollout of the vaccines has been slow, it is expected to increase rapidly. The U.S. may have 50 million to 100 million people vaccinated as early as March. That is a huge difference, one that could save many lives, especially since we also have perhaps that many people with some degree of postinfection immunity.

Here’s how to think about it: Vaccinated people are a lot less likely to get sick in the first place. One hundred million vaccinated people will mean 100 million people with much less (or hardly any) risk for any symptomatic COVID-19, especially severe disease. That’s an enormous gain.

But that’s not all. Vaccines benefit not just the vaccinated, but potentially everyone else, too. Fewer people symptomatically sick with a contagious virus means fewer sick people infecting even more people. Every indication we have suggests that vaccinated people will also transmit less—how much less is still being studied, but the difference may well be substantive. The mRNA vaccines (both already approved in the United States) cut down symptomatic disease by about 95 percent. We already know that people who never develop symptomatic disease are a lot less likely to transmit COVID-19. (Note the difference between people who are truly asymptomatic and people who are just about to get sick—presymptomatic—but are highly infectious.) In a preliminary study, the Moderna vaccine was found to even prevent two-thirds of asymptomatic infections. Vaccinated people are thus not only much, much less likely to get any disease; they appear much less likely to get even a silent, asymptomatic infection. Although we need more data to be sure, all of this strongly suggests that vaccinated people will also transmit less. The fewer people there are to efficiently transmit a pathogen, the harder it is for that pathogen to spread.

Now that we have effective vaccines, flattening the curve into the future also means obliterating the curve. Dylan Morris, a postdoc at UCLA who studies virus transmission and quantitative biology of infectious disease, and a co-author of a preprint paper studying the impact of timing on nonpharmaceutical interventions—such as reducing mobility and contacts, wearing masks, distancing, and avoiding indoor gatherings—told me that “delaying cases has always been valuable, but right now it is especially valuable. Buying even a bit of time to ramp up vaccination could avert a great deal of mortality and morbidity.” Every COVID-19 death is tragic, but with the existence of several effective vaccines, every death is now technically preventable too.

Even without a vaccine, Morris said, knocking down the virus through temporary suppression can be valuable even though the virus will grow again, precisely because of these exponential effects. The same percentage growth amounts to a much smaller number of infected people when the baseline number is much smaller. Bringing the baseline level of contagion down also allows for safer experimentation: What happens if we relax X a bit? What restrictions work best? Which ones are most sustainable? If cases are growing from a very large base number, however, that means the state of the world is changing very quickly, so small mistakes are magnified. As Morris said, “You can’t finesse the steep part of an exponential.” He noted that throughout the pandemic, we bemoaned the absence of silver bullets while underestimating the value of crude hammers. But now we are in a different situation: We do have a silver bullet—vaccines—just as we have this new threat thrown at us. How we react in the next few weeks will matter immensely.

Imagine it this way: There is a tsunami heading our way, and we are ferrying people to a high point. Everyone we transport up to the top is safe, but even better, they can also help other people get to safety (the exponential desirable effect of the vaccine). The reverse is also true, however: Everyone we leave behind also pulls down more people (the exponential unwanted effect of increased transmissibility). And the whole process is very sensitive to when we start; it’s much easier in the beginning but gets nearly impossible as the wave grows higher and gets closer. With this variant, at least in the United States, we are likely at the beginning, or near the beginning.

All this means that the speed of the vaccine rollout is of enormous importance. There are already worrisome indicators of slow rollout. Vaccination of a broad population, not vaccines in and of themselves, saves lives, and epidemics are fought with logistics and infrastructure. We should put every bit of energy, funding, and relentlessness into vaccinating as many people as possible as quickly as possible.

Meanwhile, the United States was reportedly planning to hold back half the vaccine it has in freezers as a hedge against supply-chain issues, and some states may be slowed down by murky prioritization plans. Scott Gottlieb—the former FDA chief and a current board member of Pfizer—has argued that the U.S. should also go ahead with vaccinating as many people as possible right now and trust that the supply chain will be there for the booster. Researchers in Canada—where some provinces decided to vaccinate now as much as possible without holding half in reserve, and will administer the booster with future supplies—estimate that this type of front-loading can help “avert between 34 and 42 per cent more symptomatic coronavirus infections, compared with a strategy of keeping half the shipments in reserve.” (Note that this strategy, which is different from the one the United Kingdom just announced it will adopt in prioritizing the first dose, does not even necessarily involve explicitly changing booster timing protocols in order to maximize vaccination now; it just means not waiting to get shots into arms when the vaccines are currently available.) These were already important conversations to have, but given the threat posed by this new variant, they are even more urgent.

Maybe—just maybe—this variant will turn out to be a false alarm, not nearly as transmissible as we feared. We will know soon enough. Our precautions will still be net positives. But if it is indeed much more transmissible, we may face a true tragedy: exponential growth with massive numbers of illnesses and deaths just as highly effective vaccines are being made available. We’ve had a year to learn—about the importance of early action, of acting decisively even in the face of uncertainty, of not confusing absence of evidence with evidence of absence. A year to learn to aim not for perfection in knowledge but for maximal impact even while considering the trade-offs. And most important, a year to learn to not wait when faced with threats with exponential dynamics but to act as early and as decisively as we can—and to adjust and tamper later, if warranted.

“Exponentials are so cruel that nobody wants to look them in the eye,” Morris told me. This is true, but averting our eyes doesn’t avert the outcomes. Each one of us is now counting on every person who serves the public—mayors, city-council members, health officials, nurses, FDA regulators, members of Congress, journalists—to speak up now, and to speak up loudly. We must insist on swift and aggressive action, along with more resources, in order to get this right. It is not too late. Many lives depend on what we do next.


ZEYNEP TUFEKCI is a contributing writer at The Atlantic and an associate professor at the University of North Carolina. She studies the interaction between digital technology, artificial intelligence, and society.

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India: Pune: PMC stares at staff and machinery shortage as polio and Covid vaccine drives overlap | Hindustan Times.

[Jan 04, 2021, 23:02 IST] Steffy Thevar writes:

The Pune Municipal Corporation (PMC) is likely to face a staff shortage as it is planning to begin the annual pulse polio immunisation program in tandem with the large-scale Covid vaccine drive.

India is yet to be declared a polio-free country; however, the massive pulse polio drive has gained accolades around the globe. The pulse polio drive aims to target around 3.08 lakh kids in the city alone and amidst the Covid-19 vaccination program, which is likely to go on for months, the civic body is now planning for vaccine carriers and storage facilities for both large scale immunisation programs and manpower requirements.

The pulse polio drive will begin on January 17 and will go on until January 22, 2020 during which the civic body will vaccinate 3.08 lakh kids. The first day round will primarily include vaccinating kids at the booths set up in various places while on the remaining days, kids would be vaccinated through home-to-home immunization, railway stations, bus stops and other crowded places. The civic body will have around 1,500 booths dedicated to the polio vaccine and will need 4,500 personnel to man these booths. The PMC has estimated it would need 25 cold chain equipment and 520 vaccine carriers.

The city task force meeting which met to discuss the polio immunisation drive listed the major challenges involved this year would be a shortage of manpower as schools and colleges are shut and also there is an urgent requirement of vaccine carriers. As a solution, the task force recommended that the other PMC departments especially the solid waste management and women and child departments can supply volunteers.

Dr Archana Patil, director health services, Maharashtra said, “We do not know exactly as to when the Covid-19 vaccination would start but we are preparing for our annual polio immunization program which runs for about five days and covers one crore kids in the state. We have enough cold storage capacity, walk-in freezers, walk-in coolers, ice-laced refrigerators, and vaccine carriers, but they would be engaged for the polio drive. Covid vaccination would eventually cover the entire population and would go on for months.”

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Editorials: Primary prevention of COVID‐19: advocacy for vaccination from a neurological perspective | European Journal of Neurology.

[Pay to View Full Text] [Accepted manuscript online: 01 January 2021]


Immunization by means of vaccination is a global health success story, saving millions of lives every year. In this regard, the epidemiology of measles, rabies, polio, rubella, varicella, influenza and mumps infections, all of which can harm the nervous system, could be contained by global vaccination campaigns. In addition, toxoid vaccines against bacterial toxins such as tetanus and diphtheria are indispensable and effective interventions for toxin‐mediated neurologic diseases.

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Palestinians excluded from Israeli Covid vaccine rollout as jabs go to settlers | The Guardian.

[Sun 3 Jan 2021 09.30 GMT]

Human rights groups accuse Israel of dodging obligations to millions in occupied territories who may wait months for vaccination.

Oliver Holmes in Jerusalem and Hazem Balousha in Gaza write:

Israel is celebrating an impressive, record-setting vaccination drive, having given initial jabs of coronavirus shots to more than a 10th of the population. But Palestinians in the Israeli-occupied West Bank and Gaza can only watch and wait.

As the world ramps up what is already on track to become a highly unequal vaccination push – with people in richer nations first to be inoculated – the situation in Israel and the Palestinian territories provides a stark example of the divide.

Israel transports batches of the Pfizer/BioNTech vaccine deep inside the West Bank. But they are only distributed to Jewish settlers, and not the roughly 2.7 million Palestinians living around them who may have to wait for weeks or months.

“I don’t know how, but there must be a way to make us a priority, too?” said Mahmoud Kilani, a 31-year-old sports coach from the Palestinian city of Nablus. “Who cares about us? I don’t think anybody is stuck on that question.”

Two weeks into its vaccination campaign, Israel is administering more than 150,000 doses a day, amounting to initial jabs for more than 1 million of its 9 million citizens – a higher proportion of the population than anywhere else.

Vaccine centres have been set up in sports stadiums and central squares. People over 60, healthcare workers, carers and high-risk populations have priority, while young, healthier people who walk into clinics are sometimes rewarded with surplus stock to avoid the waste of unused vials.

The prime minister, Benjamin Netanyahu, has told Israelis that the country could be the first to emerge from the pandemic. As well as a highly advanced healthcare system, part of the reason for the speed could be economics. A health ministry official said the country had paid $62 a dose, compared with the $19.50 the US is paying.

Meanwhile, the cash-strapped Palestinian Authority, which maintains limited self-rule in the territories, is rushing to get vaccines. One official suggested, perhaps optimistically, that shots could arrive within the next two weeks.

However, when asked for a timeframe, Ali Abed Rabbo, director-general of the Palestinian health ministry, estimated the first vaccines would probably arrive in February.

Those would be through a World Health Organization-led partnership called Covax, aimed at helping poorer countries, which has pledged to vaccinate 20% of Palestinians. Yet vaccines intended for Covax have not yet gained “emergency use” approval by the WHO, a precondition for distribution to begin.

Gerald Rockenschaub, the head of office at WHO Jerusalem, said it could be “early to mid-2021” before vaccines on the Covax scheme were available for distribution in the Palestinian territories.

The rest of the doses are expected to come through deals with pharmaceutical companies, but none have apparently been signed so far.

Despite the delay, the authority has not officially asked for help from Israel. Coordination between the two sides halted last year after the Palestinian president cut off security ties for several months.

But Rabbo said “sessions” with Israel had been held. “Until this moment, there is no agreement, and we cannot say there is anything practical on the ground in this regard,” he said.

Israeli officials have suggested they might provide surplus vaccines to Palestinians and claim they are not responsible for Palestinians in the West Bank and Gaza, pointing to 1990s-era interim agreements that required the authority to observe international vaccination standards.

Those deals envisioned a fuller peace agreement within five years, an event that never occurred. Almost three decades later, Israeli, Palestinian and international rights groups have accused Israel of dodging moral, humanitarian and legal obligations as an occupying power during the pandemic.

Gisha, an Israeli rights group, said Palestinian efforts so far to look elsewhere for vaccines “does not absolve Israel from its ultimate responsibility toward Palestinians under occupation”.

The disparities could potentially see Israelis return to some form of normality within the first three months of this year, while Palestinians remain trapped by the virus. That may have a negative impact on Israel’s goal of herd immunity, as thousands of West Bank Palestinians work in Israel and the settlements, which could keep infection rates up.

In Gaza, an impoverished enclave under an Israeli-Egyptian blockade, the timeframe could be even longer than in the West Bank. The strip’s Islamist rulers, Hamas, have been unable to contain the virus and are enemies with Israel and political rivals with the Palestinian Authority.

Salama Ma’rouf, head of the Hamas-run Gaza press office, estimated vaccines would arrive “within two months”, adding that there was coordination with the WHO and the Palestinian Authority.

Heba Abu Asr, 35, a resident of Gaza, jolted when asked how she felt about others getting the vaccine first. “Are you seriously trying to compare us with Israel or any other country?” she asked. “We can’t find work, food, or drink. We are under threat all the time. We do not even have any necessities for life.”

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