Study identifies seven new variants of Covid-19 in US with ‘677’ mutation
Just when you’ve heard a lot about the 3 main variants of the news cycle: the British variant (B.1.1.7), the South African variant (B.184.108.40.206) and the South American variant ( variant P.1)), and at least one mutation – E484K – which was implicated in the South African and now British variant, as well as a new “local” mutation right here in the United States, known as “677”, or more formally Q677P, recently identified by researchers in the United States
It is not known if this mutation, now identified in seven lineages or variants of Covid-19, makes it more transmissible. But there is growing concern that this potential exists.
According to a new pre-print (which has not been peer reviewed), it appears that all of these mutations impact the same region of the spike protein (amino acid position # 677) – the protruding area on the surface of the virus – which it uses to adhere to the cells it infects.
Scientists had previously looked at genomic sequences in a repository called GISAID, a global database used to exchange and share genetic sequences regarding Covid-19, but the revelation of the seven new lines or variants became apparent in late January when 2 independent SARS-CoV-2 genomic surveillance programs – the University from New Mexico in Albuquerque, and Louisiana State University Health Sciences in Shreveport – both have detected an increasing number of viruses carrying the Q677P mutation, with a significant increase in samples from late 2020 to mid-January.
One question is whether the 677 The mutation will have any impact on the ability of available vaccines to prevent “immune leakage” of neutralizing antibodies related to mutations contained in these evolving variants. We know that researchers have observed that the virus attempts to evolve in order to increase the potential for transmission and ultimately to survive.
But if a single mutation, the 677 in this case, has the ability to escape neutralizing antibodies or even increase transmission through mechanisms such as the increased ease of entry into cells via the ACE2 receptor, this remains uncertain, with some suspicion that there may still be potential. That said, an expert argues that it may be less likely.
“There is not enough information on this mutation  available, but in general it is not the case that a single mutation produces an immune breakout, ”said Amesh Adalja, MD, infectious disease physician and principal investigator at the Johns Hopkins Center for Health Security. And, with respect to the other Covid-19 mutations identified for reference, “484 [E484K] does not happen in isolation, ”he added.
However, a co-author of the pre-print, Vaughn Cooper, told CNN that the location of the mutation in the anchor region of the spike protein was in a problematic location. “The Spike stretch is important because of its proximity to a key region for virulence. We actually believe that these mutations are relatively rare (compared to other types of mutations), but they are disproportionately selected when they occur. “
Dr Jeremy Kamil, lead author of the study, told the New York Times, “I think there is a clear signature of an evolutionary advantage.” And, in this case, Kamil was referring to the process of convergent evolution coming into play – something that ultimately improves any organism’s ability to survive.
While Charles Darwin recognized convergent evolution in animals, virologists have also noted that this process can also occur in viruses, with HIV as an example when various virus species are then passed from monkeys and monkeys to humans, acquiring similar lineages of HIV as they spread among human populations.
To make it easier to describe and identify the subtypes of this mutation within the seven lineages, scientists have incorporated the names of the birds to distinguish them from one another, using names such as Robin 1, Robin 2, Yellowhammer, Pelican, Bluebird, Cail and Mockingbird.
Robin 1 has now been seen in over 30 states in the United States, primarily in the Midwest. Robin 2 appeared in early October for a sample in Alabama, confined mainly to the southeastern United States. Another line, named Pelican, was initially identified in a sample from Oregon, but was subsequently found in 12 other US states as well as in Europe (Denmark and Switzerland), Australia, as well as India.
Pelican was the first subline or variant of particular interest to researchers as it was found in nearly 28% of viral samples from Louisiana and 11% from New Mexico. The rest of the Q677P sublines each have less than 100 genetic sequences, including Yellow sparrow, mainly in the southeastern United States, Blue Bird, in the northeastern United States, Quail found in the southwest and northeast, and Mocking bird, located primarily in the south central and east coast states.
With genomic monitoring increasing, but still not widespread, the ability to identify these sublineages has been quite limited. The possibility of finding more of these variations certainly exists as surveillance increases.
“These variants were not detected until mid-August 2020, but as of February 3, 2021, they already represented more than 2,327 of the 102,462 genomes deposited at GISAID from the United States,” write the authors of the pre -impression.
This certainly deserves continued attention as genomic surveillance hopefully increases over the next few months.