spinofflive
A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)
A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)

ScienceMarch 29, 2021

As India confronts a ‘double mutation’, what is the state of Covid variants, and what do they mean for vaccines?

A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)
A nurse holds up a vial of vaccine at a hospital in Srinagar. India has administered more than 55 million shots of Covid-19 vaccine so far. (Photo: Yawar Nazir/Getty Images)

India has reported a new, double mutation coronavirus variant. Mirjam Guesgen explains what that means and what we know so far about the global variants.

What are variants?

You can think of variants a bit like breeds of dog. The variants may look different but they’re all still part of the same species so to speak (SARS-CoV-2).

Variants are when a group of mutations, changes to the genetic code, get passed down the virus family tree. When a group of coronaviruses share the same inherited set of mutations, that’s a new variant. 

How are we getting new variants?

Siouxsie Wiles and Toby Morris produced an explainer about how those mutations happen. The gist of it is when the virus makes new copies of itself inside a host cell, its genetic material gets reshuffled or changed. Those modifications in the genetic material lead to changes in proteins that make up the new virus. 

You’ll often hear scientists talking about spike proteins, those that jut out from the surface of the Covid-19 virus surface. Changes to those proteins are worth noting because those proteins help lock onto our cells and infect them, and are also the target of our body’s immune response.

Why are we getting new variants?

The mixing of genetic material is natural part of the virus copying itself but there are a number of things that can help the virus along according to University of Otago virologist Jemma Geoghegan.

For example, the more cases you have the more chance the virus has at getting better at infecting and spreading between people. 

That might be part of why we’re seeing a new variant spring up in India this past week. The Indian government is saying it’s not so much that the spike in the country’s case numbers is due to the new variant as it is the other way around, said Geoghegan. More cases made it more likely a new variant would arise.

“When you let a virus spread out of control, it’s going to evolve and it’s going to get better at infecting that host because that’s what it does,” she explained. 

How many variants are there?

There are thousands of variants popping up in different countries, but the vast majority don’t change how the virus infects us, transmits between us or causes disease, and many of them stop circulating around.

There are a handful of variants, however, where there’s evidence that they might be passed on more easily, lead to more severe disease or be harder to detect or treat. Those are the so-called variants of concern. 

Right now, the Centers for Disease Control and Prevention (CDC) in the US has identified four variants of concern: 

  1. UK variant B.1.1.7
  2. South Africa variant B.1.351 
  3. Brazil/Japan variant P.1
  4. California variant CAL.20C. 

The California one is currently limited to the US state but the others have been found worldwide. 

According to a New Zealand Ministry of Health spokesperson, “multiple variants have been documented in New Zealand, including three variants which are currently considered to be of concern.” Those being the UK, South Africa and Brazil/Japan variants.

What makes these variants spread more easily or lead to more severe disease?

Different variants have different combinations of mutations, which work in different ways to help the virus spread. 

Like variants of concern, there are also mutations of concern – ones that give the virus some kind of advantage. Those mutations are often found in several variants, which is also evidence that they’re helpful to the virus in some way. 

The UK variant for example has the N501Y mutation that helps the spike proteins cling on more tightly to the receptors on the surface of human cells. 

The South Africa variant has N501Y but also the K417N and E484K mutations. K417N interferes with the forces that push the virus away from a cell, and E484K makes the virus better at avoiding the body’s defences called neutralising antibodies, which bind to the virus to stop it entering and infecting our cells.

The Brazil/Japan variant has the tight-binding N501Y mutation and antibody-resisting E484K mutation but also the K417T mutation, which researchers think is pretty similar to the binding K417N mutation.

What is the new Indian variant?

It’s being reported as a double mutation variant. 

What does ‘double mutation variant’ mean?

It’s when a variant has two mutations of concern. It might have a bunch of other mutations too, but it has at least two that could give the virus some advantage over our defences. “The vast majority of these variants of concern are from a cluster or constellation of mutations,” says Geoghegan. 

The Indian one is a combination of mutation L452R (also in the Californian variant) and the E484Q mutation found in India. 

So what do the mutations in the new Indian variant do?

The L452R mutation is found on a spot on the virus’s genetic material that codes for binding, so researchers think it might help the virus cling more tightly to cells. It may also help the virus get around neutralising antibodies, which our body makes to try and fend off the virus from latching onto and entering our cells. They think the E484Q might also help the virus get around those neutralising antibodies. 

Are there other double mutation variants?

Technically the Brazil/Japan and South Africa variants are triple mutation variants, since they have three mutations of concern each.

Why do we care about double or triple mutation variants?

The more mutations of concern, potentially the more of an advantage the virus has over our defences. 

“The individual effects might accumulate,” said Geoghegan. “And the combination may give the virus variant an advantage over all other variants.”  

What does this mean for the vaccines?

So far there’s evidence that the Moderna and Pfizer vaccines are still effective against the UK and South Africa strains. The AstraZenica vaccine seems to work well against the UK variant but less so against the South Africa one.

There’s no research about how effective the currently-available vaccines are against the Indian variant. 

Researchers have said before that they’re confident the vaccines will work to get the body geared up to deal with the new variants. Nonetheless vaccine manufacturers may need to take extra steps like putting more than one variant (or the information for its proteins) in a jab or giving an extra booster shot.

Maxars WorldView-2 high-resolution satellite imagery of the Suez canal and the container ship. Satellite image: 2020 Maxar Technologies
Maxars WorldView-2 high-resolution satellite imagery of the Suez canal and the container ship. Satellite image: 2020 Maxar Technologies

ScienceMarch 27, 2021

How to unwedge the Suez-stranded megaship Ever Given? Think of it as a splinter

Maxars WorldView-2 high-resolution satellite imagery of the Suez canal and the container ship. Satellite image: 2020 Maxar Technologies
Maxars WorldView-2 high-resolution satellite imagery of the Suez canal and the container ship. Satellite image: 2020 Maxar Technologies

This is not a standard salvage operation: the time pressure, with ships queuing at either end of the strait, will be weighing on everyone’s minds, writes Stephen Turnock, Professor of Maritime Fluid Dynamics.

One of the world’s largest container ships, named Ever Given, has been wedged across the Suez Canal since it was blown off course by high winds in the early hours of March 23, blocking one of the busiest maritime trade corridors in the world.

The incident has created a logjam of hundreds of tankers, the operators of which are now weighing up whether to wait for the stranded container ship to be cleared, or whether rerouting around the Cape of Good Hope, at the southernmost point of Africa, will hasten their arrival at port.

That decision hinges upon how long it’ll take to refloat the Ever Given, tugging it away from the banks of the canal and back into operation. Several maritime salvage firms, with experience rescuing stricken vessels, are already in attendance at the scene – but it’s unclear how much time they’ll need to dislodge the ship.

The methods they’ll use to do so, however, will be the roughly the same as past examples. A grounded ship of any size requires additional buoyancy to help salvage crews ease it from where it’s stuck. And, in the case of the Ever Given, horizontal force – applied by tug boats – will be required to heave the ship from both banks of the Suez Canal.

How it happened

The Ever Given is 400 metres in length and has the capacity to carry over 20,000 20-foot containers. It was these containers, stacked high on the deck, that are suspected to have caught the gust of wind, like a sailboat’s sail, that ultimately blew the ship off course.

It appears that the Ever Given lost control while heading northbound along the Suez Canal, diverting its course in such a way that one end struck one of the canal’s banks. The momentum of the massive vessel will then have pulled it round until the other end struck the other bank – slowly, perhaps, but with a huge amount of force.

The precise way in which the Ever Given struck ground will be important for salvage teams to understand because, when refloating a grounded ship, it’s usually easiest to extract it the way it went in – as with a splinter.

Salvaging ships

Salvaging has always been an important part of maritime operations, with specialist companies called in when large container ships or tankers run aground. The process of freeing grounded vessels is often referred to as refloating.

In 2016, a ship of similar size to the Ever Given, called the CSCL Indian Ocean, took six days to refloat after grounding on the bank of the Elbe River in Germany. The same salvage techniques used then will be used this time around – albeit in the more restrictive environment of a narrow canal.

There are two basic approaches to extracting a grounded ship. First, salvage crews will work to increase the vessel’s vertical buoyancy force, which means the whole boat floats higher in the water.

Second, tug boats will apply sufficient horizontal force to overcome the static friction generated by whatever material the boat is resting upon. The larger and heavier the vessel, the more force required by the tug boats to refloat the ship.

Fleets of tugs

Swiftest to mobilise are a fleet of tugs, eight of which are already in position at the site of the stranded ship. But reports from the scene suggest that tugs have already attempted an unsuccessful operation to unwedge the ship.

That means the first priority of salvage teams will instead be to make the Ever Given float higher in the water – by dredging near the sections of the bank upon which the ship is stranded, and by increasing the ship’s buoyancy.

In previous salvage operations, buoyancy air bags have been attached to the underwater section of the hull to encourage it to float. But in the case of the Ever Given, this will need to happen alongside the unloading of the ship’s cargo, the removing of all on-board ballast water, and the draining of the ship’s fuel, all in an effort to make the vessel lighter and more buoyant before the tugs attempt another horizontal pull.

The removal of cargo will be particularly challenging in this case. Seeing as land access will be difficult due to the Suez Canal’s sandy surrounds, a floating crane may be required, which will take time to transport to the ship and which will only be able to remove one container at a time.

It might prove quicker to pump the fuel off the vessel instead of removing containers, which would require a small refuelling vessel to pull alongside to take on the fuel. Those overseeing the salvage will have access to computer models of the vessel to tell exactly which load-lightening strategy will be most effective.

High tide

Despite all these measures, increasing buoyancy during salvage usually relies on a rising tide, which provides an extra boost in sea level for the ship to potentially refloat upon. Unfortunately, the tidal range within the Suez Canal is limited compared to coastal waters, which will hamper refloating attempts – though a promising “spring tide”, which is higher than the usual high tide, is due over the weekend.

It’s difficult to predict the rapidity with which the various components of the salvage puzzle can be brought to bear in the Suez Canal. This is not a standard salvage operation: the time pressure, with ships queuing at either end of the strait, will be weighing on everyone’s minds.

But with expert salvage crews now on hand, and tried-and-tested refloating methods being put in place around the Ever Given, it’s likely to be only a matter of days – rather than weeks – before the ship is unwedged from the Suez Canal.The Conversation

Stephen Turnock, Professor of Maritime Fluid Dynamics, University of Southampton

This article is republished from The Conversation under a Creative Commons license. Read the original article.