Enlarge / The structure of the SARS-CoV-2 spike protein. (credit: University of Arkansas )

Over the summer, you could almost hear a sigh of relief rising from the portion of the research community that was tracking the evolution of the SARS-CoV-2 virus. Viruses, especially those new to their hosts, often pick up mutations that help them adapt to their new habitat, or they evade drugs or immune attacks. But SARS-CoV-2 seemed to be picking up mutations at a relatively sedate pace, in part because its virus-copying enzymes had a feature that lets them correct some errors.

But suddenly, new variants appear to be everywhere , and a number of them appear to increase the threat posed by the virus. A new study helps explain the apparent difference: while new base changes in the virus' genetic material remain rare, some deletions of several bases appear to have evolved multiple times, indicating that evolution was selecting for them. The research team behind this new work found evidence that these changes alter how the immune system can respond to the virus.

This looks familiar

The researchers' interest in deletions started with their involvement with an immunocompromised cancer patient, who held off the infection for over two months without being able to clear the virus. Samples obtained from late in the infection revealed two different virus strains that each had a deletion in the gene encoding the spike protein that SARS-CoV-2 uses to attach to and enter cells.

Enlarge / Picture of vials of Russia's Sputnik V vaccine against the novel coronavirus disease, COVID-19, seen at the Cotahuma Hospital in La Paz, Bolivia. (credit: Jorge Bernal/Getty Images )

Yesterday, the people behind Russia's leading vaccine, termed Sputnik V, issued a preliminary analysis of its function. The news was quite good: while the trial is ongoing and final results will have to wait, the interim data suggest that the vaccine could be over 90 percent effective.

Sputnik V is based on similar technology to the vaccines being developed by Johnson & Johnson and the Oxford/AstraZeneca collaborations. Strikingly, however, the preliminary efficiency is quite a bit higher than those vaccines are showing, and it's not clear how the Sputnik-specific features could possibly account for the difference.

Sounds great!

The results come out of a Phase III clinical trial involving roughly 21,000 participants being run in Moscow. Participants were all over the age of 18, hadn't received other vaccinations recently, weren't pregnant or drug users, and met a number of other criteria. PCR-based SARS-CoV-2 tests were performed at enrollment, and participants were also tested for the presence of antibodies against the virus.

Enlarge / Aerial view showing a tractor digging graves in a new area of the Nossa Senhora Aparecida, where COVID-19 victims are buried, in Manaus, Brazil. (credit: Marcio James / Getty Images )

While attention has been focused on the worrying new variants of SARS-CoV-2, there has been some good news: despite the evolution of a number of strains that appear to spread more readily, total COVID-19 cases have been dropping, both in the United States and globally. While there are a number of nations that are still seeing an increase in infections, a combination of reduced post-holiday spread and increased social interventions appear to be getting the surges seen in January under control.

That said, there are worrying signs that, at least in the US, a number of states are making the same mistakes that ensured that the virus never really went away after the first surge in cases. And the spread of many new variants drives home the need to avoid complacency.

Going down

The general fall in cases came up at a recent press briefing from the World Health Organization. "For the third week in a row, the number of new cases of COVID-19 reported globally fell last week," said WHO Director-General Tedros Adhanom Ghebreyesus. "There are still many countries with increasing numbers of cases, but at the global level, this is encouraging news."

Enlarge (credit: CDC.gov )

A variant of the pandemic coronavirus, SARS-CoV-2, is now dominating headlines and inspiring precautionary travel bans worldwide. But scientists are still trying to get a grip on what the variant can actually do differently and what it might mean for the nearly year-old pandemic.

Researchers in the United Kingdom—where the variant was identified and is now rapidly circulating—suggested it may be up to 70 percent more transmissible than other SARS-CoV-2 strains, stoking fear of surges-upon-surges of disease on the eve of year-end holidays. But other researchers are now rapidly working to collect data on the variant's interactions with human cells and immune responses to see if those interactions differ from those seen by other SARS-CoV-2 strains.

What we know

While much remains to be known about the variant, dubbed B.1.1.7, there are some reassuring aspects. For one thing, it's normal for viruses to accumulate the small genetic changes, such as those that created the new UK variant (more on that below). Many other variants have been identified throughout the pandemic, and none has spawned any nightmare scenarios.

Enlarge / MOSCOW, RUSSIA - SEPTEMBER 4, 2020: Medical staff with newly delivered boxes containing COVID-19 vaccine in a cold room at No2 Outpatient Clinic in southern Moscow. (credit: Stanislav Krasilnikov / Getty Images )

Russia has been one of the countries hit hard by the COVID-19 pandemic. But its response to that has been a bit... unusual. As many other countries have, Russia worked to develop its own vaccine. But while that development was still in progress, it announced that it wasn't going to wait for detailed safety data , and instead roll the vaccine out to millions. Shortly afterwards, it became clear that the country was actually going to run a standard phase 3 clinical trial , albeit a large one, involving 40,000 people.

It was hard to judge whether any of this was reasonable, because few details of the vaccine itself were available. But that changed somewhat on Friday, as the people who developed the vaccine published the results of the initial clinical trials. And so far, it seems to be about as effective as some of the other ones that have been made it past initial trials.

Two viruses better than one?

As our earlier coverage mentioned, the vaccine is composed of two different engineered viruses. These contain the backbone of an innocuous virus, called an adenovirus, engineered to include the gene that encodes the major surface protein from the SARS-CoV-2 virus. This protein, called Spike, is what the coronavirus uses to latch on to and enter cells. The use of adenovirus allows the immune system to learn to recognize the Spike protein while the body only experiences a harmless adenovirus infection.

Enlarge / The Wuhan Institute of Virology in Wuhan in China's central Hubei province on April 17, 2020. (credit: Getty | Hector Retamal )

A New York-based nonprofit that has worked for decades to better understand and prevent the type of coronavirus pandemic now engulfing the world was abruptly stripped of its federal research funding in April. The White House specifically directed the National Institutes of Health to cancel the multimillion-dollar research grant after President Donald Trump promoted an unfounded conspiracy theory that the pandemic coronavirus, SARS-CoV-2, was released from a lab in Wuhan, China—a lab that collaborates with the nonprofit.

Now, the NIH has told the nonprofit, EcoHealth Alliance, that it may have its funding back—if it collects and hands over materials and information about the Chinese lab, which is part of the Wuhan Institute of Virology (WIV).

In a July 8 letter seen by The Wall Street Journal , the NIH laid out a list of seven criteria EcoHealth Alliance must fulfill in order to regain its peer-reviewed funding. The list includes: