What’s the new coronavirus variant in India and how should it change their COVID response?


Prafulla Shriyan, Indian Institute of Public Health, Gandhinagar and Giridhara R Babu, Indian Institute of Public Health, GandhinagarAfter genome sequencing of over 10,000 COVID-19 cases in India, researchers have discovered a new variant with two new mutations which may be better at evading the immune system.

In 15-20% of samples from the Indian state of Maharashtra (the state accounting for 62% of cases in the country) a new, double mutation in key areas of the virus has been detected. These are now known as the E484Q and L452R mutations.

What makes the variant different?

Both these mutations are concerning because they are located in a key portion of the virus – the spike protein – that it uses to penetrate human cells. Spike proteins attach via a “receptor binding domain”, meaning the virus can attach to receptors in our cells.

These new mutations include changes to the spike protein that make it a “better fit” for human cells. This means the virus can gain entry more easily and multiply faster. Given what we have seen with other similar mutations, it might also make it harder for our immune system to recognise the virus due to its slightly different shape. This means our immune system may not be able to recognise the virus as something it has to produce antibodies against.

The emergence of these new variants has only been possible because of the continued viral replication in areas with high circulation.

Though the Indian government has said the data on the variants circulating in India (including this new Indian variant and others including the UK strain) are not sufficient to link them to the rapid increase in the number of cases in the country, we think it’s the most likely explanation. The country had managed to bring down the rate in February, but a sudden increase in the number of reported cases is now being reported.




Read more:
What’s the difference between mutations, variants and strains? A guide to COVID terminology


Implications

The implications of these developments are greatly concerning – not just for India, but for the rest of the world. Mutations can result in 20% more in-hospital deaths, as we witnessed during the second wave in South Africa. This is because some mutant variants have the ability to spread faster, resulting in sudden surges and, therefore, an overburdened health system.

But there’s hope. Places around the world with higher vaccination coverage such as the UK and Israel are witnessing a steady decrease in cases.

Most of the currently approved vaccines around the world have been found to evoke an immune response to some extent against multiple variants. But no trials have yet been undertaken on the effectiveness of vaccines against these new Indian mutations.

To make it difficult for the mutant strains to develop vaccine resistance, we have to ensure wider and faster vaccine coverage across the world.

What has to happen now?

Apart from vaccine manufacturers’ efforts to update the composition of vaccines to better deal with new strains, it is important to contain transmission across the world. Countries can use the World Health Organisation’s SARS-CoV-2 Risk Monitoring and Evaluation Framework to help identify, monitor and assess variants of concern, swiftly.




Read more:
Yes, the coronavirus mutates. But that shouldn’t affect the current crop of vaccines


To establish a direct link between a variant and a steep rise in cases in a short time, it is important to use genomic sequencing to link clusters together. But unless contact tracing is done meticulously, it isn’t easy to do so.

It is also important to understand the mechanisms involved in the infectiousness and virulence of the newer variants. For this, lab models are needed to mimic spread and virulence mechanisms efficiently.

To combat the consequences of mutations in India, its pandemic response will have to incorporate several measures. Genomic surveillance will have to be proactive and coincide with the epidemiological investigation of the cluster of cases for early identification and swift action.

As some variants can escape naturally induced immunity, vaccine manufacturers in India will need to develop better vaccines to cover these new variants. Ongoing surveillance and containment measures need to be strengthened to prevent the emergence of new variants by minimising viral replication.

And finally, swift and rapid vaccine coverage is not only necessary but essential for ensuring any modest levels of success in tackling this pandemic.




Read more:
The UK variant is likely deadlier, more infectious and becoming dominant. But the vaccines still work well against it


The Conversation


Prafulla Shriyan, Research Fellow, Public Health Foundation of India, Indian Institute of Public Health, Gandhinagar., Indian Institute of Public Health, Gandhinagar and Giridhara R Babu, Professor, Head-Lifecourse Epidemiology, Indian Institute of Public Health, Indian Institute of Public Health, Gandhinagar

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

The UK variant is likely deadlier, more infectious and becoming dominant. But the vaccines still work well against it


Kirsty Short, The University of Queensland

New research published this week in the British Medical Journal found the coronavirus variant originating in the United Kingdom, called B.1.1.7, is substantially more deadly than the original strain of SARS-CoV-2.

The authors say the B.1.1.7 variant is between 32 and 104% deadlier. However, it’s important to recognise these data were only collected from one group of people so more research is needed to see if these numbers hold true in other groups of patients.

The B.1.1.7 variant is becoming the dominant virus in many parts of the world, and is more infectious than the original strain (UK authorities have suggested it’s up to 70% more transmissible). This makes sense because a virus can become more transmissible as it evolves. However, it’s actually a strange thing for a virus to become more deadly over time (more on that later).

The good news is preliminary data suggest COVID vaccines still perform very well against this variant.

What did the study find?

There are two ways to check if someone has this variant. The first is by doing full genomic sequencing, which takes time and resources. The other, easier way, is to analyse results from the standard PCR test, which normally takes a swab from your nose and throat.

This test targets two viral genes in the swab sample, one of which doesn’t work very well with this variant (it’s called the “S-gene”). So if someone was positive for one of these genes, but negative for the “S-gene”, there’s a good chance they’re infected with the B.1.1.7 variant.

The study authors looked at the S-gene status of 109,812 people with COVID, and looked at how many died. They found S-gene negative people had a higher chance of dying 28 days after testing positive for the virus. The study “matched” patients in the S-gene positive and S-gene negative groups based on various factors (including age) to ensure these factors didn’t confound the results.




Read more:
UK, South African, Brazilian: a virologist explains each COVID variant and what they mean for the pandemic


This matches a report from the UK government’s New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG), which said in January there’s a “realistic possibility” infection with this strain is linked with a higher chance of death.

With increased death from a variant, you would also expect to see increased hospitalisations and ICU admissions in places where the variant is surging. We’re still waiting for better data on this, but one Danish study suggested an increased risk of hospitalisation from this variant.

But why is it more deadly?

Viruses have a selective advantage (meaning they’re more likely to outcompete other viruses) if they’re able infect more hosts. It’s also advantageous for the virus if they can evade the host’s immune response, because it helps them survive longer and reproduce more.

But it’s actually quite strange for this variant to be more deadly. There’s not a selective advantage for a virus to kill its host, because it might kill its host before they transmit the virus.

Scientists still need to find out why this variant is more deadly, and how it came about.

One possibility is this variant’s increased disease severity is linked to its increased transmissibility. For example, it could be that because it’s more infectious, it’s leading to larger clusters of infection including in places like aged care homes, which we know are linked to more deaths. We don’t know for sure yet.

Vaccines still respond well to this variant

It’s important to note the current crop of vaccines still perform well against the variant.

A slight drop in the numbers of neutralising antibodies responding to the B.1.1.7 virus was recorded after vaccination with vaccines from Novavax and Moderna. But the protection these vaccines offer should still be sufficient to prevent severe disease. This variant also had a negligible impact on the function of T-cells, which can kill virus-infected cells and help control the infection.

Preliminary data suggest people given the AstraZeneca vaccine also experienced a mild decrease in the number of circulating antibodies when infected with the B.1.1.7 variant. But again, the effect was relatively modest, and the authors say the efficacy of the vaccine against this variant is similar to that of the original Wuhan strain of the virus.




Read more:
COVID-19 vaccine FAQs: Efficacy, immunity to illness vs. infection (yes, they’re different), new variants and the likelihood of eradication


It’s becoming dominant

The B.1.1.7 variant is becoming the dominant strain in many parts of the world. The ABC reports it’s dominant in at least 10 countries.

In the UK it represents around 98% of new cases, and up to 90% of new cases in some parts of Spain.

In Denmark, new cases from this variant were around 0.3% in November last year, rising to 65% of new cases in February. It accounts for more than two-thirds of new cases in the Netherlands.

In the United States, the states of Florida, Texas and California (among others) are seeing significant increases in the number of cases from this variant.

It’s possible the spread of this variant is even higher than reported. The ability to detect its spread is dependent on how often genomic sequencing is done, and many countries aren’t currently in the position to do regular genomic testing.

There’s a suggestion from some researchers and commentators the variant is linked with a surge in cases among kids. However, this observation remains largely anecdotal and it’s unclear if this simply reflects rising total case numbers in certain places.The Conversation

Kirsty Short, Senior Lecturer, The University of Queensland

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

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TURKEY: ANCIENT MONASTERY THREATENED


Muslims’ legal action against 1,600-year-old structure called ‘malicious.’

ISTANBUL, January 22 (Compass Direct News) – Syriac Christians in southeastern Turkey say a land dispute over the historic Mor Gabriel Monastery is part of a larger system of discrimination against the religious minority in this overwhelmingly Islamic country.

Muslim residents of southeastern Turkey dispute the boundary lines of an ancient Christian monastery dating to the fourth century as being unnecessarily large for the needs of a religious community. Islamic village leaders from Yayvantepe, Eglence and Candarli are attempting to confiscate one-third of the monastery’s property, claiming it was wrongfully appropriated and that they need it for their livestock.

Area Muslims also say the land in question is forest and thereby registered as land belonging to the State Treasury.

“Our land is being occupied by the monastery,” said Ismail Erlal, village leader of Yayvantepe, according to Cihan News Agency. “We make use of the forest there and pasture our animals; we won’t give up our rights.”

Among the most contentious issues are the monastery walls built around its perimeter, rebuilt 15 years ago. Village leaders complain in a lawsuit to obtain the land that the monastery has gone beyond its rightful bounds. In August the land survey office of Midyat said it had determined that 270 hectares of the monastery’s 760 hectares were government property, including land inside and outside the monastery’s walls.

A court in Mardin originally scheduled a hearing for Friday (Jan. 16) to determine the legal status of the monastery walls, but it was rescheduled to Feb. 11 to allow the court more time to examine the case. At the February hearing the court will determine if the 270 hectares of land belong to the government or the monastery.

Metropolitan Timotheos Samuel Aktas, leader of the monastery, answered in a report that the monastery has the right to leave its land uncultivated and has paid taxes on the property since 1937.

The state originally charged the monastery with being founded illegally, but it dropped those charges by canceling a hearing originally schedule for Dec. 24. Rudi Sumer, the attorney representing the monastery, said that the claim was groundless since the monastery has foundation status dating back to modern Turkey’s origins, not to mention centuries of existence beforehand.

The mayors of Yayvantepe, Eglence and Candarli also charged the monastery with attempting to proselytize young children (illegal in Turkey) and carrying out “anti-Turkish” activity.

Metropolitan Aktas said in a report that these claims were groundless and of the same provocative nature that has historically sparked violence against Turkey’s Christians.

“All the allegations are frivolous and vexatious, devoid of any logic or evidence, solely aimed with the malicious intent of rousing anti-Christian sentiments by the surrounding Muslim villages,” he said.

 

Europe Watching

Mor Gabriel Monastery, founded in 397, is the most revered monastery for Syrian Orthodox Christians. It is inhabited by 15 nuns and two monks and is the seat of Metropolitan Bishop of Tur Abdin Diocese.

In recent decades the monastery has turned into a religious and social center for the country’s remaining Syriacs by offering schooling to children and teaching their ancient language of Syriac, a variant of the language spoken by Jesus.

“The monastery is everything for us,” said a Syrian Orthodox Christian who grew up in Turkey’s southeast. He added that many families in the area had named their children after Mor Gabriel. “Syriacs would give up everything for the monastery.”

An international outcry from the European Parliament and numerous Assyrian organizations throughout Europe arose in response to the charges, according to the Assyrian International News Agency. A member of the German consulate said his country would monitor the case closely, as Turkey is attempting to join the European Union and its human rights record has come under close scrutiny.

Many Syrian Orthodox Christians have left southeast Turkey in the last 30 years as violence escalated between the military and Kurdish terrorists. In the last five years, however, some Syriacs have begun returning home – only to find their property occupied by others.

Residents who fled Mardin province in the mid-1980s returned to find two of their village’s Syriac churches converted into mosques. And the demographic shift from Syriacs to Kurds has increased pressure on the monastery.

“Turkey must protect its Assyrian community,” said Swedish parliamentarian Yilmaz Kerim to the Hurriyet Daily News. He visited the monastery as part of a delegation in December. “There are only 3,000 left in Midyat.”

The lawsuit has the support of a local parliamentarian who claims Christians relished their opportunity to leave Turkey. Süleyman Çelebi, member of the ruling Justice and Development Party (AKP), said Syrian Orthodox Christians had never come under pressure, despite their claim that they were exploited, and even emigrated away from Turkey “with joy” in previous decades.

The three villages that brought the lawsuit against the monastery overwhelmingly supported the Islamic-rooted AKP in last year’s national elections. Çelebi claims that the official boundaries of the monastery were established in Ottoman times but not properly observed by the Syriac Christians.

According to the 1923 Lausanne Treaty, Turkey grants full protection to churches, synagogues and other religious establishments to freely practice their own religions. But this treaty only designated Greek and Armenian Orthodox Christians and Jews, creating complications for groups such as the Syrian Orthodox and Protestants to open schools and churches.

Syriac Christians claim to be one of the first people to accept Christianity in the Middle East. Their historic homeland stretches through southeastern Turkey, but their numbers have dwindled to 15,000 following decades of government pressure and fallout from war against the Kurdistan Workers’ Party.  

Report from Compass Direct News