After appearing to do a remarkable job containing and controlling the COVID-19 epidemic in that nation even as the disease spiked elsewhere, an increase in cases that began in March overturned the “India miracle.” With confirmed cases exceeding 400,000 per day during several days in May, India shattered the previous U.S. records for daily cases. And with a national shortage of testing materials and a positive rate above 25%, there’s no doubt those horrific numbers greatly underestimate the number of actual cases.
The death counts in India have also been ghastly. For more than a week, the official tally has topped 4,000 COVID-related deaths per day, and reliable sources on the ground have made it clear this vastly underestimates the true number of deaths as fires from makeshift cremation sites burn in fields and parking lots 24/7. Earlier this week, multiple outlets reported that hundreds of bodies had washed up along the banks of the Ganges River, thrown there after even mass cremation failed to dispose of all the dead.
One the one hand, it’s easy to single out a big driving force behind the explosion of cases in India: Prime Minister Narendra Modi all but eliminated social distancing guidelines and even promoted large gatherings as India moved into campaign season. Modi gave his blessing not only to large campaign rallies, but a massive religious pilgrimage that saw millions come from across the country to the now body-laden Ganges.
However, there’s good evidence that the explosion of cases in India isn’t just a sign of bad decisions and bad timing. Because the variant that’s exploding across that nation may be a serious threat to the world.
The website CoVariants.org is maintained by Swiss virologist Dr. Emma Hodcroft. The site catalogs the “variants” of interest—mostly those with significant changes to the SARS-CoV-2 spike protein—as they are found in nations around the world. Hodcroft gives the data a fascinating presentation by turning each nation’s array of variants into a chart that shows change over time.
For example, here are the variants found in the U.K. from the outset of the pandemic to date.
COVID-19 variants in the U.K. (orange = older European variant, red — U.K. B.1.1.7 variant)
On this infographic, the orange area represents the variant of COVID-19 that emerged out of Europe in the first days of the pandemic to become the most common version in most regions, including the United States. That version is also dominant in the U.K. over much of the pandemic, until the B.1.1.7 variant appears in the fall—that’s the dark red area on the graph. With astounding rapidity, the new variant replaces the old, giving good evidence to estimates that the B.1.1.7 variant is 50-70% more contagious than older variants. It swamps everything … until that little green wedge appears in the last few weeks. We’ll get back to that.
COVID-19 variants in Germany (red = B.1.1.7)
Across Europe, the story seems very similar to that of the U.K. A variety of variants are found, many of them seeming to be comparable to the original variant. Then B.1.1.7 appears and clobbers them all. As an example, Germany shows a number of variants, several of which are parts of the B.1.160 (or EU2) family. Then all that variety gets buried under a sea of red as the U.K. variant arrives.
COVID-19 variants in the United States
The story in the United States is a little more complicated. First, sampling for COVID-19 variants in the United States was both late and inadequate. That purple variant that becomes dominant by the fall is the home-grown one that was first located in California. The lighter lavender color is a spin-off from that initial variant now known as B.1.526 which was first identified in New York. That version contains the E484 mutation, making it a variant of concern because that mutation is known to increase vaccine evasion and is known to have been involved in at least one case of reinfection.
If you’re wondering about the lighter-colored variant expanding at the top of the U.S. chart, that’s the Brazil P.1 variant. It’s definitely a concern as well … just not the focus of today’s worryfest.
At the very bottom of the right side of the U.S. chart, so narrow that it’s difficult to see, is something that just arrived in this county—a tiny slice of green. And now, as promised, here’s why that’s important.
COVID-19 variants in India are in green
In India, the story goes like this: Near the start of the pandemic, cases appear bearing the genetic signature of the European variant. For the most part, India is able to hold off a major spike in cases until the fall, at which time samples in the nation are divided about half and half between that variant and the U.K. variant, which shows up in Indian samples in November, about a month after it first appears in the U.K.
Only as cases in India began to skyrocket in the early spring, it’s not the U.K. variant that’s driving out all the rest, it’s two new variants driving out the U.K. variant. These variants—the light and dark green above—are known as B.1.617. They’re members of the “Pango lineage” of variants. The B.1.617.2 version (dark green above), contains both the spike protein change that was found in the California variant (purple on the U.S. chart) and a mutation called P681 which is poorly understood, but may make it more difficult to antibodies to recognize and attack the virus.
Everything about the B.1.617.2 variant is poorly understood at the moment, but one thing should be clear from the chart above: It’s out-competing the B.1.1.7 variant. In samples taken in India at the start of the year, B.1.1.7 was 10 times more prevalent than the then recently discovered B.1.617 variant. In the latest full week sampled, the two B.1.617 variants outpaced cases based on B.1.1.7 by eight times.
All of this may sound like gobbledygook of the highest order, and the various naming systems of viral clades doesn’t make it any less difficult to relay. But think of it like this:
The original European variant that swept over Italy, France, and the Northeastern U.S. around the time the pandemic became a pandemic was likely about 50% more contagious than the version that first appeared in the Wuhan district of China. The U.K. variant that has displaced that European variant in many countries show that the U.K. variant is somewhere around 50-70% more contagious than the European variant. Now these new variants are outcompeting the U.K. variant in India. Meaning they may be considerably more contagious than the U.K. variant.
Of course, this could be a fluke. There could be special circumstances within India that advantaged the B.1.617 variants. One example does not a trend make.
That’s where that little green wedge in the U.K. chart comes in. That wedge represents the arrival of the B.1.617.2 variant in the U.K. Back at the end of February, this variant appeared in a handful of cases. By the first of April, it accounted for just 1% of the cases examined in the U.K. Then, just 10 days later, it had increased to 8%.
None of these numbers are super solid, because no nation is really sampling at the rate required to well-define the genetic mix of COVID-19 variants present. That’s particularly true of both India and the U.S., where the term “sucks” doesn’t begin to describe just how bad the system has been across the pandemic. But just to drive things home, let’s look at one more chart.
COVID-19 variants in Singapore
Singapore is on of those places that, for the most part, has done fantastically well throughout the pandemic. It fought back a spike in spring 2020 that saw 27 deaths. Since then, over the course of more than a year, just four more people have died in the nation. A lot of this has come from Singapore’s traditional “Disneyland with a death penalty” administration, where the government doesn’t hesitate to tell you exactly how to run your life and “conformity is the prime directive.”
But the pattern of new cases in Singapore reflects what seems to be happening in several less clinically managed nations across the region: B.1.617.2 is rapidly becoming the dominant strain of COVID-19.
Earlier this month, Dr. Francis Collins, director of the National Institute of Science, announced that lab testing showed that the current generation of vaccines in use in the United States—Pfizer/ BioNTech, Moderna, and Johnson & Johnson—were all “effective against the B.1.617 variant.” But, said Collins, it was “a little less effective” against that variant than others.
The concern here is that the variant sweeping India, the one producing deaths more rapidly than people have been able to burn people’s bodies despite conscripting parks and parking lots as crematoria, is considerably more contagious than even the highly contagious B.1.1.7 variant. How much more contagious, we don’t know. It’s also more evasive than other variants. Exactly how much, we don’t know. It may also be more virulent, that is, more likely to cause serious illness or death. We don’t know.
We don’t know a lot of things about B.1.617. But we do know that there’s a lot of it out there, case counts are growing, and it would make a horrible starting point for a SARS-CoV-2 variant that checks every box for “worse.”
Over the past week, the seven-day-moving average of new COVID-19 cases in the United States has moved to its lowest level in 408 days, unwinding the awful meter all the way back to April 1, 2020. That sharp decline in new cases is surely playing a role in an announcement that could come at any time over the next week.
The CDC is expected to announce this week that those who have been fully immunized against COVID-19 no longer need to wear masks or practice social distancing in most locations, including indoors. However, everyone should continue to honor requests to mask up by business or other venues.
There is no word yet on whether this might extend to relaxing mask guidelines on public transportation.
Updated CDC guidance
The death counts in India have also been ghastly. For more than a week, the official tally has topped 4,000 COVID-related deaths per day, and reliable sources on the ground have made it clear this vastly underestimates the true number of deaths as fires from makeshift cremation sites burn in fields and parking lots 24/7. Earlier this week, multiple outlets reported that hundreds of bodies had washed up along the banks of the Ganges River, thrown there after even mass cremation failed to dispose of all the dead.
One the one hand, it’s easy to single out a big driving force behind the explosion of cases in India: Prime Minister Narendra Modi all but eliminated social distancing guidelines and even promoted large gatherings as India moved into campaign season. Modi gave his blessing not only to large campaign rallies, but a massive religious pilgrimage that saw millions come from across the country to the now body-laden Ganges.
However, there’s good evidence that the explosion of cases in India isn’t just a sign of bad decisions and bad timing. Because the variant that’s exploding across that nation may be a serious threat to the world.
The website CoVariants.org is maintained by Swiss virologist Dr. Emma Hodcroft. The site catalogs the “variants” of interest—mostly those with significant changes to the SARS-CoV-2 spike protein—as they are found in nations around the world. Hodcroft gives the data a fascinating presentation by turning each nation’s array of variants into a chart that shows change over time.
For example, here are the variants found in the U.K. from the outset of the pandemic to date.
COVID-19 variants in the U.K. (orange = older European variant, red — U.K. B.1.1.7 variant)
On this infographic, the orange area represents the variant of COVID-19 that emerged out of Europe in the first days of the pandemic to become the most common version in most regions, including the United States. That version is also dominant in the U.K. over much of the pandemic, until the B.1.1.7 variant appears in the fall—that’s the dark red area on the graph. With astounding rapidity, the new variant replaces the old, giving good evidence to estimates that the B.1.1.7 variant is 50-70% more contagious than older variants. It swamps everything … until that little green wedge appears in the last few weeks. We’ll get back to that.
COVID-19 variants in Germany (red = B.1.1.7)
Across Europe, the story seems very similar to that of the U.K. A variety of variants are found, many of them seeming to be comparable to the original variant. Then B.1.1.7 appears and clobbers them all. As an example, Germany shows a number of variants, several of which are parts of the B.1.160 (or EU2) family. Then all that variety gets buried under a sea of red as the U.K. variant arrives.
COVID-19 variants in the United States
The story in the United States is a little more complicated. First, sampling for COVID-19 variants in the United States was both late and inadequate. That purple variant that becomes dominant by the fall is the home-grown one that was first located in California. The lighter lavender color is a spin-off from that initial variant now known as B.1.526 which was first identified in New York. That version contains the E484 mutation, making it a variant of concern because that mutation is known to increase vaccine evasion and is known to have been involved in at least one case of reinfection.
If you’re wondering about the lighter-colored variant expanding at the top of the U.S. chart, that’s the Brazil P.1 variant. It’s definitely a concern as well … just not the focus of today’s worryfest.
At the very bottom of the right side of the U.S. chart, so narrow that it’s difficult to see, is something that just arrived in this county—a tiny slice of green. And now, as promised, here’s why that’s important.
COVID-19 variants in India are in green
In India, the story goes like this: Near the start of the pandemic, cases appear bearing the genetic signature of the European variant. For the most part, India is able to hold off a major spike in cases until the fall, at which time samples in the nation are divided about half and half between that variant and the U.K. variant, which shows up in Indian samples in November, about a month after it first appears in the U.K.
Only as cases in India began to skyrocket in the early spring, it’s not the U.K. variant that’s driving out all the rest, it’s two new variants driving out the U.K. variant. These variants—the light and dark green above—are known as B.1.617. They’re members of the “Pango lineage” of variants. The B.1.617.2 version (dark green above), contains both the spike protein change that was found in the California variant (purple on the U.S. chart) and a mutation called P681 which is poorly understood, but may make it more difficult to antibodies to recognize and attack the virus.
Everything about the B.1.617.2 variant is poorly understood at the moment, but one thing should be clear from the chart above: It’s out-competing the B.1.1.7 variant. In samples taken in India at the start of the year, B.1.1.7 was 10 times more prevalent than the then recently discovered B.1.617 variant. In the latest full week sampled, the two B.1.617 variants outpaced cases based on B.1.1.7 by eight times.
All of this may sound like gobbledygook of the highest order, and the various naming systems of viral clades doesn’t make it any less difficult to relay. But think of it like this:
The original European variant that swept over Italy, France, and the Northeastern U.S. around the time the pandemic became a pandemic was likely about 50% more contagious than the version that first appeared in the Wuhan district of China. The U.K. variant that has displaced that European variant in many countries show that the U.K. variant is somewhere around 50-70% more contagious than the European variant. Now these new variants are outcompeting the U.K. variant in India. Meaning they may be considerably more contagious than the U.K. variant.
Of course, this could be a fluke. There could be special circumstances within India that advantaged the B.1.617 variants. One example does not a trend make.
That’s where that little green wedge in the U.K. chart comes in. That wedge represents the arrival of the B.1.617.2 variant in the U.K. Back at the end of February, this variant appeared in a handful of cases. By the first of April, it accounted for just 1% of the cases examined in the U.K. Then, just 10 days later, it had increased to 8%.
None of these numbers are super solid, because no nation is really sampling at the rate required to well-define the genetic mix of COVID-19 variants present. That’s particularly true of both India and the U.S., where the term “sucks” doesn’t begin to describe just how bad the system has been across the pandemic. But just to drive things home, let’s look at one more chart.
COVID-19 variants in Singapore
Singapore is on of those places that, for the most part, has done fantastically well throughout the pandemic. It fought back a spike in spring 2020 that saw 27 deaths. Since then, over the course of more than a year, just four more people have died in the nation. A lot of this has come from Singapore’s traditional “Disneyland with a death penalty” administration, where the government doesn’t hesitate to tell you exactly how to run your life and “conformity is the prime directive.”
But the pattern of new cases in Singapore reflects what seems to be happening in several less clinically managed nations across the region: B.1.617.2 is rapidly becoming the dominant strain of COVID-19.
Earlier this month, Dr. Francis Collins, director of the National Institute of Science, announced that lab testing showed that the current generation of vaccines in use in the United States—Pfizer/ BioNTech, Moderna, and Johnson & Johnson—were all “effective against the B.1.617 variant.” But, said Collins, it was “a little less effective” against that variant than others.
The concern here is that the variant sweeping India, the one producing deaths more rapidly than people have been able to burn people’s bodies despite conscripting parks and parking lots as crematoria, is considerably more contagious than even the highly contagious B.1.1.7 variant. How much more contagious, we don’t know. It’s also more evasive than other variants. Exactly how much, we don’t know. It may also be more virulent, that is, more likely to cause serious illness or death. We don’t know.
We don’t know a lot of things about B.1.617. But we do know that there’s a lot of it out there, case counts are growing, and it would make a horrible starting point for a SARS-CoV-2 variant that checks every box for “worse.”
CDC expected to declare mask freedom for the vaccinated
Over the past week, the seven-day-moving average of new COVID-19 cases in the United States has moved to its lowest level in 408 days, unwinding the awful meter all the way back to April 1, 2020. That sharp decline in new cases is surely playing a role in an announcement that could come at any time over the next week.
The CDC is expected to announce this week that those who have been fully immunized against COVID-19 no longer need to wear masks or practice social distancing in most locations, including indoors. However, everyone should continue to honor requests to mask up by business or other venues.
There is no word yet on whether this might extend to relaxing mask guidelines on public transportation.
Updated CDC guidance