Virus World

Highly efficacious vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed. However, the emergence of viral variants that are more infectious than the earlier SARS-CoV-2 strains is concerning. Several of these viral variants have the potential to partially escape neutralizing antibody responses warranting continued immune-monitoring. Here, we tested a number of currently circulating viral variants of concern/interest, including B.1.526 (Iota), B.1.1.7+E484K (Alpha), B.1.351 (Beta), B.1.617.2 (Delta) and C.37 (Lambda) in neutralization assays using a panel of post-mRNA vaccination sera. The assays were performed with authentic SARS-CoV-2 clinical isolates in an assay that mimics physiological conditions.

We found only small decreases in neutralization against B.1.526 and an intermediate phenotype for B.617.2. The reduction was stronger against a sub-variant of C.37, followed by B.1.351 and B.1.1.7+E484K. C.37 is currently circulating in parts of Latin America and was detected in Germany, the US and Israel. Of note, reduction in a binding assay that also included P.1, B.1.617.1 (Kappa) and A.23.1 was negligible. Taken together, these findings suggest that mRNA SARS-CoV-2 vaccines may remain effective against these viral variants of concern/interest and that spike binding antibody tests likely retain specificity in the face of evolving SARS-CoV-2 diversity.

Preprint Available in medRxiV (July 23, 2021):

https://doi.org/10.1101/2021.07.21.21260961 

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."

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.

Four-fifths of symptomatic cases develop fevers, more than in earlier outbreaks. The findings match trends in other countries where the Delta variant is spreading.  As the Delta variant of the coronavirus spreads in southeastern China, doctors say they are finding that the symptoms are different and more dangerous than those they saw when the initial version of the virus started spreading in late 2019 in the central city of Wuhan. Patients are becoming sicker and their conditions are worsening much more quickly, doctors told state-run television on Thursday and Friday. Four-fifths of symptomatic cases developed fevers, they said, although it was not clear how that compared with earlier cases. The virus concentrations that are detected in their bodies climb to levels higher than previously seen, and then decline only slowly, the doctors said. Up to 12 percent of patients become severely or critically ill within three to four days of the onset of symptoms, said Guan Xiangdong, director of critical care medicine at Sun Yat-sen University in the city of Guangzhou, where the outbreak has been centered. In the past, the proportion had been 2 percent or 3 percent, although occasionally up to 10 percent, he said. Doctors in Britain and Brazil have reported similar trends with the variants that circulated in those countries, but the severity of those variants has not yet been confirmed.

The testimonies from China are the latest indication of the dangers posed by Delta, which the World Health Organization last month labeled a “variant of concern.” First identified this spring in India, where it was blamed for widespread suffering and death, Delta has since become the dominant variant in Britain, where doctors suggest that it is more contagious and may infect some people who have received only one of two doses of a Covid-19 vaccine. China has uniquely detailed data, however, because it has essentially universal testing in the vicinity of outbreaks, allowing officials to gather detailed information on the extent of cases. Delta’s spread in southeastern China focuses more attention on the effectiveness of China’s self-made vaccines. The Chinese authorities have not indicated how many of the new infections have occurred in people who had been vaccinated. In some other countries where Chinese-made vaccines are in wide use, including the Seychelles and Mongolia, infections among vaccinated people are rising, although few patients have reportedly developed serious illness. Nearby Shenzhen had a handful of cases last week of the Alpha variant, which first emerged in Britain.

As some other parts of the world still struggle to acquire and administer large numbers of coronavirus tests, southeastern China has used its local production of scarce chemicals to conduct testing on a remarkable scale. The authorities said that they had conducted 32 million tests in Guangzhou, which has 18 million people, and 10 million in the adjacent city of Foshan, which has seven million.

Guangzhou has also isolated and quarantined tens of thousands of residents who had been anywhere near those infected. The testing and quarantine appear to have slowed but not stopped the outbreak. China’s National Health Commission announced on Friday that nine new cases had been found in Guangzhou the previous day. “The epidemic is not over yet, and the risk of virus transmission still exists,” said Chen Bin, deputy director of the Guangzhou Municipal Health Commission.

Under-30s to be offered jabs from next week but variant makes decision on easing rules in England ‘more difficult’.  The new Delta variant of coronavirus appears to be about 40% more transmissible than the variant it has largely replaced, Matt Hancock has said, making government decisions about whether to ease restrictions in England on 21 June “more difficult”. Saying that under-30s in England will be called to begin vaccinations from next week, the health secretary confirmed it was still possible the reopening programme could be delayed or some rules kept in place. “We consider all options,” he told Sky News. The transmissibility of the Delta variant, first identified in India, has been seen as a central factor to the decisions over whether to remove most remaining restrictions in England in a fortnight, with the decision due to be made later this week. Estimates have said the Delta variant could be anywhere between 30% and 100% more transmissible than the so-called Alpha variant first identified in Kent. But asked for the latest information, Hancock gave a figure of 40%. “That means that it is more difficult to manage this virus with the new Delta variant,” he said. “But crucially, after two doses of vaccine we are confident that you get the same protection that you did with the old variant. So the good news is that the vaccine still works just as effectively.” It was, he said, still too early to decide what might happen on 21 June: “The prime minister and I and the team will be looking at all of the data over this week … The critical thing is to see whether the four tests we have set have been met.” Saying the Covid vaccination programme had “severed but not broken” the link between infection rates and hospitalisations, Hancock said adults under 30 would be able to seek first injections from next week.

When the first cases of the SARS-CoV-2 Delta variant were detected in the United Kingdom in mid-April, the nation was getting ready to open up. COVID-19 case numbers, hospitalizations and deaths were plummeting, thanks to months of lockdown and one of the world’s fastest vaccination programmes. Two months later, the variant, which was first detected in India, has catalysed a third UK wave and forced the government to delay the full reopening of society it had originally slated for 21 June. After observing the startlingly swift rise of the Delta variant in the United Kingdom, other countries are bracing for the variant’s impact — if they aren’t feeling it already. Nations with ample access to vaccines, such as those in Europe and North America, are hopeful that the shots can dampen the inevitable rise of Delta. But in countries without large vaccine stocks, particularly in Africa, some scientists worry that the variant could be devastating. “In my mind, it will be really hard to keep out this variant,” says Tom Wenseleers, an evolutionary biologist and biostatistician at the Catholic University of Leuven (KU Leuven) in Belgium. “It’s very likely it will take over altogether on a worldwide basis.”  Delta, also known as B.1.617.2, belongs to a viral lineage first identified in India during a ferocious wave of infections there in April and May. The lineage grew rapidly in some parts of the country, and showed signs of partial resistance to vaccines. But it was difficult for researchers to disentangle these intrinsic properties of the variant from other factors driving India’s confirmed cases past 400,000 per day, such as mass gatherings.

Delta data

The Delta variant has been linked to a resurgence of COVID-19 in Nepal, southeast Asia and elsewhere, but its UK spread has given scientists a clear picture of the threat it poses. Delta seems to be around 60% more transmissible than the already highly infectious Alpha variant (also called B.1.1.7) identified in the United Kingdom in late 2020. Delta is moderately resistant to vaccines, particularly in people who have received just a single dose. A Public Health England study published on 22 May found that a single dose of either AstraZeneca's or Pfizer's vaccine reduced a person’s risk of developing COVID-19 symptoms caused by the Delta variant by 33%, compared to 50% for the Alpha variant. A second dose of the AstraZeneca vaccine boosted protection against Delta to 60% (compared to 66% against Alpha), while two doses of Pfizer’s jab were 88% effective (compared to 93% against Alpha). Preliminary evidence from England and Scotland suggests that people infected with Delta are about twice as likely to end up in hospital, compared with those infected with Alpha. “The data coming out of the UK is so good, that we have a really good idea about how the Delta variant is behaving,” says Mads Albertsen, a bioinformatician at Aalborg University in Denmark. “That’s been an eye-opener.” Denmark, which, like the United Kingdom, is a world leader in genomic surveillance, has also seen a steady rise in cases caused by the Delta variant — although far fewer than most other European countries. It is only a matter of time before the variant becomes dominant in Denmark, says Albertsen, but the hope is that its expansion can be slowed through vaccination, surveillance and enhanced contact tracing. “It’s going to take over,” he says, but “hopefully in a few months and not too soon.” Meanwhile, the Danish government is easing restrictions, not re-imposing them: restaurants and bars have been open for months to individuals who have been vaccinated or received a recent negative test, and, as of 14 June, masks are no longer required in most indoor settings. “It is looking good now in Denmark, and we are keeping a close eye on the Delta variant,” says Albertsen. “It can change quite fast, as it has done in the UK.” Cases of the Delta variant in the United Kingdom are doubling roughly every 11 days. But countries with ample vaccine stocks should be reassured by the slower uptick in hospital admissions, says Wenseleers. A recent Public Health England study1 found that people who have had one vaccine dose are 75% less likely to be hospitalized, compared with unvaccinated individuals, and those who are fully protected are 94% less likely to be hospitalized. 

US spread

Delta is also on the rise in the United States, particularly in the Midwest and southeast. The US Centers for Disease Control and Prevention declared it a variant of concern on 15 June. But patchy surveillance means the picture there is less clear. According to nationwide sampling conducted by the genomics company Helix in San Mateo, California, Delta is rising fast. Using a rapid genotyping test, the company has found that the proportion of cases caused by Alpha fell from more than 70% in late April to around 42% as of mid-June, with the rise of Delta driving much of the shift2. Jeremy Kamil, a virologist at Louisiana State University Health in Shreveport, expects Delta to eventually become dominant in the United States, “but to be somewhat blunted by vaccination”. However, vast disparities in vaccination rates could lead to regional and local variation in cases and hospitalizations caused by Delta, says Jennifer Surtees, a biochemist at the University at Buffalo, New York, who is conducting regional surveillance. She notes that 70% of eligible New Yorkers have received at least one dose of vaccine — a milestone that triggered the lifting of most COVID-19 restrictions last week — but that figure is below 40% in some parts of the state. Communities with high proportions of African American and Hispanic individuals, where vaccination rates tend to be low, could be especially hard hit by Delta. “These are populations that are really at risk of a localized outbreak from Delta, so I think it’s really important to still keep tracking and watch this as much as possible,” Surtees says. Data from Helix2 on nearly 20,000 samples sequenced since April suggest that the Delta variant is spreading faster in US counties where less than 30% of residents have been fully vaccinated, compared to the counties with vaccination rates above that threshold.

Africa at risk

Delta poses the biggest risk, scientists say, to countries that have limited access to vaccines, particularly those in Africa, where most nations have vaccinated less than 5% of their populations. “The vaccines will never come in time,” says Wenseleers. “If these kinds of new variant arrive, it can be very devastating.” Surveillance in African countries is extremely limited, but there are hints that the variant is already causing cases there to surge. Several sequences of the variant have been reported in the Democratic Republic of the Congo, where an outbreak in the capital city of Kinshasa has filled hospitals. The variant has also been detected in Malawi, Uganda and South Africa. Countries that have close economic links to India, such as those in East Africa, are probably at the greatest risk of seeing a surge in cases caused by Delta, says Tulio de Oliveira, a bioinformatician and director of the KwaZulu-Natal Research and Innovation Sequencing Platform in Durban, South Africa. In his country, all of the Delta cases have been detected in shipping crews at commercial ports, with no signs yet of spread in the general community. De Oliveira expects it to stay this way. South Africa is in the middle of a third wave of infections caused by the Beta variant (also known as B.1.351) identified there last year. This, combined with a lack travel from countries affected by Delta, should make it harder for a new variant to take hold. Similar factors could be keeping Delta at bay in Brazil, which is battling another immune-evading variant called P.1, or Gamma, says Gonzalo Bello, a virologist at the Oswaldo Cruz Institute in Rio de Janeiro, who is part of a team conducting national surveillance. So far, Brazil has sequenced just four cases of the Delta variant in the country. While countries gird themselves against the Delta variant — or hope that it passes them by — researchers say we need to watch for even greater threats. “What most people are concerned about are the next variants — if we start to see variants that can really challenge the vaccines,” says Albertsen.

Published in Nature (June 22, 2021):

https://doi.org/10.1038/d41586-021-01696-3

The Centers for Disease Control and Prevention (CDC) yesterday said that Delta, a highly transmissible COVID-19 variant first identified in India and currently sweeping through the United Kingdom, now makes up at least 10% of all US cases. On May 22, the variant had made up only 2.7% of cases.The CDC also now designated Delta as a variant of concern, which means the agency officially recognizes that the variant may carry a risk of more severe illness and transmissibility. In addition to Delta, the CDC has noted five other variants of concern. The rapid rise of the variant in the United Kingdom—where it now accounts for 90% of cases—has slowed that nation’s reopening efforts by 4 or 5 weeks.

See variant distribution in the U.S.A:

https://covid.cdc.gov/covid-data-tracker/#variant-proportions