Virus World

The delta variant, first detected in India a little less than a year ago, now represents 99% of sequenced Covid-19 cases globally.

• Almost all of the up to 900,000 Covid cases sequenced worldwide over the last 60 days originated from the delta strain, Maria Van Kerkhove, the WHO’s technical lead on Covid, said.
• Europe accounted for roughly 60% of the more than 3.3 million new cases in the world last week, Van Kerkhove said.
• Covid cases worldwide have been increasing over the last four consecutive weeks, she added. 

The delta variant, first detected in India a little less than a year ago, now represents 99% of sequenced Covid-19 cases globally, making it more prevalent than any other strain, officials from the World Health Organization said Tuesday. Almost all of the up to 900,000 Covid cases sequenced worldwide over the last 60 days originated from the delta strain, Maria Van Kerkhove, the WHO’s technical lead on Covid, said during a Q&A streamed on the organization’s social media channels. Van Kerkhove’s comments come amid an international increase in Covid infections driven by surging cases in Europe. The Continent accounted for roughly 60% of the more than 3.3 million new cases in the world last week, Van Kerkhove said. “Delta is really the dominant one,” Van Kerkhove said. “And there are two variants of interest – mu and lambda – that we’ve been tracking as well, but again, where delta is present, delta takes over.”   

Van Kerkhove said Europe represented more than half of the just under 50,000 global Covid deaths in the last week, a 5% increase in fatalities across the Continent. Covid cases worldwide have been increasing over the last four consecutive weeks, she added. “The pandemic is heading in the wrong direction at the moment,” Van Kerkhove said. The decreased use of masks and social distancing are to blame for Europe’s surge, Van Kerkhove said at a briefing last week. She cautioned Tuesday that societies reopening across the Northern Hemisphere this winter could lead to a rise in respiratory illnesses over the months ahead, including influenza and other pathogens. Select European countries are bearing the brunt of the surge. Germany set a record seven-day average of nearly 39,300 new cases on Monday, up almost 40% from the week before, according to a CNBC analysis of data from Johns Hopkins University. The U.K. tallied a weekly average of more than 38,500 new cases Monday, an increase of 13% from the previous week. Seven-day averages in France and Italy were both up by nearly 40% as well. Russia also saw a pandemic high seven-day average of roughly 1,199 deaths on Monday, Johns Hopkins reported. But its seven-day average case count, over 38,000 infections, decreased by more than 2%.

In parts of the country with low vaccination rates, the variant may be responsible for up to 90% of sequenced cases, officials said. The rapidly spreading Delta variant now accounts for 83% of sequenced Covid-19 cases in the United States, the nation’s public health leaders said Tuesday, and in parts of the country with low vaccination rates, it may be responsible for up to 90%.  Rochelle Walensky, the director of the Centers for Disease Control and Prevention, told a congressional hearing the new 83% estimate represents “a dramatic increase” from 50% of sequenced cases that were tallied the week of July 3. In some parts of the country that percentage is even higher, particularly in areas with low vaccination rates, said Anthony Fauci, head of the National Institute of Allergy and Infectious Diseases. As the variant has spread, Covid-19 deaths in the U.S. have risen, climbing by nearly 48% over the past week and now averaging 239 per day, she said.  “We know the majority of deaths could be prevented by vaccination,” Walensky said. Vaccination has been uneven, with levels below half of eligible people in two-thirds of the country, Walensky said. She cited a five-month CDC study that found 99.5% of Covid-19 deaths are among people who are unvaccinated. 

“The best way to prevent the spread of Covid-19 variants is to prevent the spread of disease. And vaccination is the most powerful tool we have,” she said. “We must continue to expand vaccine coverage by building trust and confidence in Covid-19 vaccines. And this is particularly important in communities of color, rural communities, and other population groups at risk.” Pressed to explain why the U.S. has not pursued booster shots as Israel has done with third Pfizer doses, Walensky and Fauci both pushed back. Walensky said the CDC is sharing data with Israel and the U.K. “where they’re several weeks ahead of us in the variant,” while watching more than 20 cohorts of vaccine recipients for any signs that their protection against Covid-19 might be waning. So far protection from recognizable disease continues to hit percentages in the low 90s, Fauci said. “If you see it fall below that into the 80s or even, unfortunately, I hope it never happens, into the 70s, then, you know, you reach the point where the durability needs a boost,” he said. “Those studies are ongoing right now.” Fauci blamed the variant’s high transmissibility for the surge in cases among unvaccinated people. First identified in India, Delta has swept through 90 countries around the world. But the three vaccines approved in the U.S. — mRNA vaccines from Moderna and Pfizer and the adenovirus-delivered vaccine from Johnson & Johnson — continue to be highly effective against Delta and other variants. “We have the tools to end this epidemic,” Fauci told the Senate Committee on Health, Education, Labor and Pensions. “It’s up to us to use those tools to the maximum.”

The number of confirmed COVID-19 cases attributed to the highly contagious Delta variant jumped 66 per cent in Canada this week.

Canada’s chief public health officer Dr. Theresa Tam said as of Friday there are just over 2,000 confirmed cases of the variant. Just three days ago, the Public Health Agency told The Canadian Press there were 1,187 confirmed cases. “The Delta variant is now in all provinces and at least one of our territories,” Tam said at the House of Commons health committee. “Of course, as with all coronavirus cases, we may not know every single case that has occurred in Canada, hence my warning of precaution and the need to get two doses of vaccine into as many people as possible.” The variant was first identified in India but has now become the dominant strain in the United Kingdom where it is spreading rapidly, mostly among unvaccinated people. It is believed to be at least 1.5 times as contagious as the Alpha variant first identified in the U.K. Alpha is, for now, the dominant variant in Canada, with more than 216,000 cases confirmed. Public Health England reported Friday the number of confirmed Delta cases in the U.K. had grown 80 per cent in the last week, to almost 76,000. British Prime Minister Boris Johnson had to delay plans to fully lift all public health restrictions next week, with plans to keep the final limitations in place at least another month. 

Tam says the variant is a concern because one dose of vaccine isn’t as effective against it and it underscores the need for Canada to keep picking up the pace on second doses. Two doses of the vaccines Canada is using are believed to offer very good protection against Delta, and even one dose has been found to be good at preventing serious illness. All provinces are warning against the existence of Delta. It is believed to be the driver of a major outbreak at the Kashechewan First Nation in northern Ontario, is involved in an outbreak at a Calgary hospital, and is worrying health officials in Waterloo, Ont., which is suddenly the province’s COVID-19 hot spot. Data on the variant in Canada, however, is limited and it hasn’t yet been added to the Health Canada website reporting variant cases. Only Alpha, Beta (the B. 1.351 variant identified in South Africa, and Gamma (the P. 1 variant first identified in Brazil), are listed on Canada’s website.  That site also hasn’t adjusted the names to use the Greek alphabet now preferred by the World Health Organization. A spokeswoman for Health Canada told The Canadian Press in early June that Delta would be added to it in “the coming weeks.” When asked again this week, the same answer was provided. Dr. Howard Njoo, the deputy chief public health officer, said data gathering on the variant hasn’t been easy and there is a lag in reporting. “There are obviously some issues we need to work on,” he said, noting there “are probably more cases” than we have seen reported. He said, however, the data provinces and territories do have suggest most of the Delta cases are being found in people who aren’t vaccinated.

Background

The B.1.617.2 (delta) variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (Covid-19), has contributed to a surge in cases in India and has now been detected across the globe, including a notable increase in cases in the United Kingdom. The effectiveness of the BNT162b2 and ChAdOx1 nCoV-19 vaccines against this variant has been unclear.

Methods

We used a test-negative case–control design to estimate the effectiveness of vaccination against symptomatic disease caused by the delta variant or the predominant strain (B.1.1.7, or alpha variant) over the period that the delta variant began circulating. Variants were identified with the use of sequencing and on the basis of the spike (S) gene status. Data on all symptomatic sequenced cases of Covid-19 in England were used to estimate the proportion of cases with either variant according to the patients’ vaccination status.

Results

Effectiveness after one dose of vaccine (BNT162b2 or ChAdOx1 nCoV-19) was notably lower among persons with the delta variant (30.7%; 95% confidence interval [CI], 25.2 to 35.7) than among those with the alpha variant (48.7%; 95% CI, 45.5 to 51.7); the results were similar for both vaccines. With the BNT162b2 vaccine, the effectiveness of two doses was 93.7% (95% CI, 91.6 to 95.3) among persons with the alpha variant and 88.0% (95% CI, 85.3 to 90.1) among those with the delta variant. With the ChAdOx1 nCoV-19 vaccine, the effectiveness of two doses was 74.5% (95% CI, 68.4 to 79.4) among persons with the alpha variant and 67.0% (95% CI, 61.3 to 71.8) among those with the delta variant.

Conclusions

Only modest differences in vaccine effectiveness were noted with the delta variant as compared with the alpha variant after the receipt of two vaccine doses. Absolute differences in vaccine effectiveness were more marked after the receipt of the first dose. This finding would support efforts to maximize vaccine uptake with two doses among vulnerable populations. (Funded by Public Health England.)

Published in NEJM (July 21, 2021):

https://doi.org/10.1056/NEJMoa2108891 

What is the delta plus variant of SARS-CoV-2? Learn how it differs from the delta variant, why it is a variant of concern, and whether vaccines work against it. A novel SARS-CoV-2 variant, the delta plus variant, has been identified in over 10 countries. Health authorities are raising concerns that the variant may have an increased ability to transmit, but they also note that this variant’s transmissibility is likely similar to that of the preexisting delta variant.  As ever more SARS-CoV-2 variants emerge, governments and public health experts continue to consider the best strategies to contain their spread. There are currently 11 variants of the SARS-CoV-2 virus that the World Health Organization (WHO)Trusted Source is monitoring. One of these variants, the delta variant — also known as the B.1.617.2 lineage — was first identified in India in December 2020 and quickly became the most common variant in the country. It has demonstrated 40–60% increased transmission, in comparison with the previously dominant alpha variant, and is currently the dominant SARS-CoV-2 variant in the United Kingdom.

Meanwhile, researchers recently identified another variant — the delta plus variant, also known as B.1.617.2.1 or AY.1. The U.K. governmental agency Public Health England first declared it a “variant of concern” in a June 11 briefing, and on June 22, Indian authorities followed suit. Since then, 11 countries have reported a collective 197 cases of COVID-19 caused by the delta plus variant of SARS-COV-2. The delta plus variant is a sublineage of the delta variant, with the only known difference being an additional mutation, K417N, in the virus’ spike protein, the protein that allows it to infect healthy cells. This mutation is also found in the beta and gamma variants, which researchers first identified in South Africa and Brazil, respectively.

The WHO shared with Reuters that “For the moment, this variant does not seem to be common, currently accounting for only a small fraction of the delta sequences.” Yet, “Delta and other circulating variants of concern remain a higher public health risk, as they have demonstrated increases in transmission,” the WHO added. Furthermore, since India has labeled this variant a “variant of concern,” the country’s SARS-CoV-2 Consortium on Genomics (INSACOG), which is made up of 28 laboratories dedicated to whole genome sequencing of the SARS-CoV-2 virus and its evolving variants, continues to follow the evolution of delta plus. INSACOG lists the following concerns regarding the delta plus variant:

• increased transmissibility
• stronger binding to receptors of lung cells
• potential reduction in monoclonal antibody response

The spike protein is responsible for binding to a cell’s surface receptors, allowing the virus to enter. A mutation in the protein may strengthen this interaction, which could increase transmissibility, as per these first two points.

This mutation, however, is present in other variants, as well, so it is likely not a new source of concern. Additionally, virologist Dr. Jeremy Kamil, from the Louisiana State University Health Sciences Center, suggested to the BBC that “Delta plus might have a slight advantage at infecting and spreading between people who were previously infected earlier during the pandemic or who have weak or incomplete vaccine immunity.” But he also noted that this is not much different from the delta variant. Other experts have also raised the third point, about the variant’s potential to reduce the effectiveness of monoclonal antibody treatments. These include therapies such as the bamlanivimab and etesevimab and REGN-COV2 combination therapies, which researchers have shown to be beneficial in treating mild to moderate COVID-19 when given early during the course of the disease. However, this reduced effectiveness “is not a major difference, as the therapy itself is investigational and few are eligible for this treatment,” said epidemiologist and vaccine expert Dr. Chandrakant Lahariya in a CNBC interview.

With concerns surrounding the Delta coronavirus variant rising globally, how effective are the current vaccines in the U.S. at protecting against the new version of the virus? According to medical experts, the three vaccines currently available each offer protection. Here’s a breakdown of each vaccine and what you should know: How effective are the COVID vaccines overall? In clinical trials, Moderna’s  In clinical trials, Moderna's vaccine reported 94.1% effectiveness at preventing COVID-19 in people who received both doses. The Pfizer-BioNTech vaccine was said to be 95% effective. A new CDC study reported that a single dose of Pfizer's or Moderna's COVID vaccine was 80% effective in preventing infections. That number jumped to 90% two weeks after the second dose, the study on vaccinated health care workers showed.  "These findings indicate that authorized mRNA COVID-19 vaccines are effective for preventing SARS-CoV-2 infection, regardless of symptom status, among working-age adults in real-world conditions," the U.S. agency wrote in the study. "COVID-19 vaccination is recommended for all eligible persons." Pfizer's vaccine, the only one currently authorized for use in children as young as 12, also showed heightened effectiveness among adolescents.  Pfizer in late March released preliminary results from a vaccine study of 2,260 U.S. volunteers ages 12 to 15, showing there were no cases of COVID-19 among fully vaccinated adolescents compared with 18 among those given dummy shots. More intriguing, researchers found the kids developed higher levels of virus-fighting antibodies than earlier studies measured in young adults. The FDA said J&J’s vaccine offers strong protection against what matters most: serious illness, hospitalizations and death. One dose was 85% protective against the most severe COVID-19 illness, in a massive study that spanned three continents — protection that remained strong even in countries such as South Africa, where the variants of most concern were spreading at the time.  The CDC reports J&J/Janssen vaccine was 66.3% effective in clinical trials at preventing COVID-19 illness in people who had no evidence of prior infection 2 weeks after receiving the vaccine. "The vaccine had high efficacy at preventing hospitalization and death in people who did get sick," the CDC notes. "No one who got COVID-19 at least four weeks after receiving the J&J/Janssen vaccine had to be hospitalized." It is not known if any of the three vaccines prevent the spread of the virus by people who are asymptomatic, though the CDC noted that "early evidence suggests that the J&J/Janssen vaccine might provide protection against asymptomatic infection." 

How effective are the vaccines against the new Delta variant?

Data surrounding vaccine effectiveness with the Delta variant is so far limited. While studies have shown that the available vaccines work against variants, including the Delta variant, all two-dose vaccines offer significantly more protection following their second dose. Researchers in England studied how effective the two-dose AstraZeneca and Pfizer-BioNTech vaccines were against it, compared with the Alpha variant that was first detected in the U.K. The vaccines were protective for those who got both doses but were less so among those who got one dose. One recent study showed the Pfizer vaccine was 84% effective against the variant after two doses, but only 34% effective after the first dose.  Moderna also announced Tuesday that a new study showed its vaccine also produced promising protection in a lab setting against the Delta variant and others currently circulating. “As we seek to defeat the pandemic, it is imperative that we are proactive as the virus evolves. We remain committed to studying emerging variants, generating data and sharing it as it becomes available. These new data are encouraging and reinforce our belief that the Moderna COVID-19 Vaccine should remain protective against newly detected variants,” Stéphane Bancel, chief executive officer of Moderna, said in a statement. Currently, little data has been released showing just how effective the Johnson & Johnson is at protecting against the Delta variant, though it is believed that the single-shot vaccine does offer protection against the variant. Dr. Scott Gottlieb, former Food and Drug Administration commissioner, reportedly said the Johnson & Johnson vaccine appears to be about 60% effective against the Delta variant. Still, medical experts say any of the three vaccines currently being used in the U.S. continue to show good results as far as protection. ”This will protect them against getting very sick and being hospitalized and even dying from the Delta variant,” Dr. Katherine Gergen-Barnett of Boston Medical Center recently told NBC10 Boston.

Will a booster shot be needed?

So far, there has been no recommendation from the Centers for Disease Control and Prevention surrounding booster shots with the Delta variant. Still, health experts have repeatedly cautioned that COVID-19 booster shots could be needed for fully vaccinated people, particularly as new variants spread. White House chief advisor Dr. Anthony Fauci said during an interview with MSNBC's Medhi Hasan in April that people may need to get booster shots in a year.  Pfizer CEO Albert Bourla also previously said people will "likely" need a third dose within 12 months of getting fully vaccinated.  So far, studies suggest that the vaccines currently in use can recognize the emerging variants — but they may not provide quite as much protection against the new strains. Boosters and new versions of vaccines that target the variants are already being explored. Pfizer-BioNTech was previously testing a third booster shot of its vaccine on fully vaccinated people.   "The flexibility of our proprietary mRNA vaccine platform allows us to technically develop booster vaccines within weeks, if needed," Sahin said in a release in February. Moderna was also testing a potential third dose of its current vaccine, and a possible booster shot specifically targeting the South Africa variant. Citing early data, the company recently said the booster vaccine generated a promising immune response against the B.1.351 and P.1 variants first identified in South Africa and Brazil, respectively. Meanwhile, Johnson & Johnson CEO Alex Gorsky said during an interview with CNBC's "Squawk Box" in March that the company is well-positioned to adapt its vaccine for variants, and is working on developing software that will "help address some of these new and emerging variants."