New Covid-19 Variants Detected

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Ravinda Gupta, an infectious diseases consultant at the hospital and a clinical microbiologist at the University of Cambridge said, “We saw some remarkable changes in the virus over that time” when referring to the treatment of an elderly patient. The patient was treated for 101 days and 23 different swab samples were taken.  Gupta continued, “We saw mutations that seemed to suggest the virus was showing signs of adaptation to avoid the antibodies in the convalescent plasma treatment. It was the first time we had seen something like this happening in a person in real time.”

For a little bit of technical details, one of the identified mutations was a deletion of two amino acids – known as H69 and V70 – in the spike protein.  Gupta said of the matter, “We did some infection experiments using artificial viruses and they showed that the H69/V70 deletion mutation increases the infectivity by twofold.” This was the start of the discovery that a new variant is causing a large outbreak. 

Wendy Barclay, a virologist at Imperial College London and a member of the UK’s New and Emerging Respiratory Virus Threats Advisory Group said, “We were not missing cases but it is unusual to see two of the tests working but a third not.”  Rising cases in the UK were confusing doctors and scientists.  The problem is that most of the tests we are familiar with at this stage are targeting a sequence on the spike protein.  The tests were sometimes failing to pick up on the mutation – a deletion at the same H69 and V70 positions in the protein seen by Gupta. When discovering this, they also found an entire lineage of 16 other mutations, now designated as B1117 – the British Covid-19 variant.

Michael Worobey, a viral evolutionary biologist at the University of Arizona said, “To me these seem like a glimpse into the future where we are going to be in an arms race with this virus, just like we are with flu.”  Brendan Larsen, a PhD student working with Worobey in Arizona says, “It is hard to speculate, but it is interesting that all of a sudden there does seem to be a lot of mutations appearing that could be associated with immune escape or immune recognition.” Larsen has recently identified a new variant of the virus in Arizona that has the same amino acid deletion.  Because this mutation is happening in different parts of the world, and through millions of people, there are reasons to believe it may be evolving in specific ways.

Larsen says, “By themselves they are likely to have a minor impact overall.  But together all of these different mutations might make it more difficult for the immune system to recognize the virus.”  Larsen and Worobey believe this could lead to even more patients catching the virus a second time, and that changes to the vaccine may need to be made.

More variants have also been identified – 20C-US by researchers in Illinois, V1176F and D614G by scientists at the University of Manitoba in Winnipeg, Canada, and S477N discovered by scientists in Australia. 

“The first letter in these mutation names indicates the amino acid that has been replaced, the number is its location on the protein, and the final letter is the new amino acid that has appeared at that site.”

To scientists, the evolution and mutations are not surprising.  This happens with most viruses and bacteria.  Carolyn Williamson, head of the division of virology at the University of Cape Town says, “I do not see a reason that this evolutionary selective process would differ in a pandemic such as Sars-CoV-2 [the Covid-19 virus], compared to a geographically contained epidemic.”  The concern however is that there could be other versions around the world where the testing materials needed to detect them are not available.  Larsen says, “If new variants emerge in a country where there isn’t much genome sequencing, it could be a real problem.”

For more updates be sure to check back with the ABN Blog regularly.

For a little bit of technical details, one of the identified mutations was a deletion of two amino acids – known as H69 and V70 – in the spike protein.  Gupta said of the matter, “We did some infection experiments using artificial viruses and they showed that the H69/V70 deletion mutation increases the infectivity by twofold.” This was the start of the discovery that a new variant is causing a large outbreak. 

Wendy Barclay, a virologist at Imperial College London and a member of the UK’s New and Emerging Respiratory Virus Threats Advisory Group said, “We were not missing cases but it is unusual to see two of the tests working but a third not.”  Rising cases in the UK were confusing doctors and scientists.  The problem is that most of the tests we are familiar with at this stage are targeting a sequence on the spike protein.  The tests were sometimes failing to pick up on the mutation – a deletion at the same H69 and V70 positions in the protein seen by Gupta. When discovering this, they also found an entire lineage of 16 other mutations, now designated as B1117 – the British Covid-19 variant.

Michael Worobey, a viral evolutionary biologist at the University of Arizona said, “To me these seem like a glimpse into the future where we are going to be in an arms race with this virus, just like we are with flu.”  Brendan Larsen, a PhD student working with Worobey in Arizona says, “It is hard to speculate, but it is interesting that all of a sudden there does seem to be a lot of mutations appearing that could be associated with immune escape or immune recognition.” Larsen has recently identified a new variant of the virus in Arizona that has the same amino acid deletion.  Because this mutation is happening in different parts of the world, and through millions of people, there are reasons to believe it may be evolving in specific ways.

Larsen says, “By themselves they are likely to have a minor impact overall.  But together all of these different mutations might make it more difficult for the immune system to recognize the virus.”  Larsen and Worobey believe this could lead to even more patients catching the virus a second time, and that changes to the vaccine may need to be made.

More variants have also been identified – 20C-US by researchers in Illinois, V1176F and D614G by scientists at the University of Manitoba in Winnipeg, Canada, and S477N discovered by scientists in Australia. 

“The first letter in these mutation names indicates the amino acid that has been replaced, the number is its location on the protein, and the final letter is the new amino acid that has appeared at that site.”

To scientists, the evolution and mutations are not surprising.  This happens with most viruses and bacteria.  Carolyn Williamson, head of the division of virology at the University of Cape Town says, “I do not see a reason that this evolutionary selective process would differ in a pandemic such as Sars-CoV-2 [the Covid-19 virus], compared to a geographically contained epidemic.”  The concern however is that there could be other versions around the world where the testing materials needed to detect them are not available.  Larsen says, “If new variants emerge in a country where there isn’t much genome sequencing, it could be a real problem.”

For more updates be sure to check back with the ABN Blog regularly.

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