COVID-19 News : Scientist are concerned over the new SARS-CoV-2 variant that emerged in Manaus, Brazil called P.1 that has more mutations on it than even the UK variant called B.1.1.7 or even the South African Variant called B.1.351 as it could change the course of the current pandemic if it starts becoming prevalent.
The new P.1 variant lineage carries 17 unique amino acid changes, 3 deletions, and 4 synonymous mutations, and one 4nt insertion compared to the most closely related available non-P.1 sequence (EPI_ISL_722052), which lies at the base of the long branch immediately ancestral to P.1. The P.1 lineage meets the criteria for new lineage designation on the basis that it is phylogenetically and genetically distinct from ancestral viruses, associated with rapid spread in a new area, and carries a constellation of mutations that may have functional and/or phenotypic relevance. https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586
The spike protein itself contains 10 mutations! Among these are the E484K and N501Y mutations.
Scientists are speculating that the new variant is not only more infectious and able to evade the human host immune system but is also like to be more deadly based on what is currently happening in Manaus, Brazil where those infected are displaying more severe stages of the disease and more are dying from infections there.
Emerging variants of the coronavirus have been in the news ever since scientists raised the alarm over B.1.1.7, a SARS-CoV-2 variant that first caught scientists’ attention in England in December and that is more transmissible than previously circulating viruses.
However now, they’re also focusing on a potential new threat: variants that could do an end run around the human immune response. Such “immune escapes” could mean more people who have had COVID-19 remain susceptible to reinfection, and that proven vaccines may, at some point, need an update.
Detailed research is currently underway and the various mutations found on the new variant are being studies. It is also speculated that the current COVID-19 vaccines will not be able to have any effect on this new variant.
The P.1 variant is affecting travel to South America as effort is made to prevent its spread. Meanwhile, areas of Brazil are experiencing surging numbers of COVID-19 cases and oxygen supplies are running out.
Health authorities in Japan notified the World Health Organization (WHO) of their concern over a new SARS-CoV-2 variant on 9 January after detecting it in airport tests from four travelers from Brazil. Whole-genome sequencing detected the variant. https://www.thailandmedical.news/news/breaking-covid-19-news-japan-discovers-new-sars-cov-2-variant-originating-from-brazil,-the-b-1-1-248-variant-with-12-spike-mutations
This new detected variant came from the B.1.1.248 lineage. Its
mutations include the N501Y mutation, which it has in common with the variants reported by South Africa and the UK, and the E484K. This is the second variant detected from Brazil containing the E484K mutation.
The World Health Organization is currently working with both Japan and Brazil to evaluate the variant, determining if this variant is more severe, has higher transmission, or if it could be detrimental to current therapies, diagnostics or vaccines for the disease. https://www.who.int/news/item/12-01-2021-global-scientists-double-down-on-sars-cov-2-variants-research-at-who-hosted-forum
Meanwhile across the world, many countries are developing their own teams to monitor variants and their effect; for example, the UK launched their G2P-UK job today, a group consisting of scientists from a broad spectrum of specialties working to evaluate new variants and their potential effects on vaccines or transmissibility.
Currently COVID-19 cases in Brazil are surging exponentially and hospitals are running out of space and oxygen. The situation has reached new levels in Manaus, a city in the Amazonas state, where patients have had to be transported out of their hospitals due to severe oxygen shortage. The new variant, detected by the Japanese authorities, was traced back to this region of Brazil.
The lack of help and supplies will result in many deaths as the situation becomes more desperate and healthcare workers send out pleas for oxygen supplies.
Detailed research is needed to determine if this variant is going to increase negative public health concerns. At the moment there is no evidence of any variants that cause more severe illness or that render the current vaccines ineffective.
Phylogenetic tree of the B.1.1.28 lineage rooted by its earliest genome (2020-03-05). A. Sequences generated in this study are highlighted in orange (n=18) and red (n=13, P.1. lineage). B. Phylogenetic tree highlighting the P.1 lineage containing the Manaus sequences and closely related sequences, including those from subclade AM-II. Inset in grey: the unique set of mutations from the P.1 lineage in comparison with its nearest sequence (EPI_ISL_722052). The scale of the phylogenetic branches is given as substitutions per nucleotide site.
As with the UK and South Africa variant, the Brazilian variant appears to have mutations in its spike protein that may make it more highly transmissible.
Furthermore there is also concern that the South African and Brazilian variants may carry a mutation allowing them to evade some of human’s natural immune responses, although more research is needed to confirm this. If this is the case, it could reduce their response to the current vaccines.
Numerous countries have started to enforce protective measures against the introduction of the variant, with the UK suspending arrivals from South America, Panama, Cape Verde and Portugal.
Mutations and new variants will continue to occur as the pandemic continues. The more it spreads, the more chance it has to mutate, and the more chance a mutation will affect the current vaccines.
The World health Organization is advising all countries to increase testing the sequencing of SARS-CoV-2 viruses where possible and to share sequence data internationally, so that changes in the virus can be monitored.
To date how these new variants are affecting the course of the pandemic is still unclear. In Manaus, for example, P.1 might have nothing to do with the new surge in infections; people’s immunity might simply be waning, says Oxford epidemiologist Dr Oliver Pybus.
In a press conference last week, WHO’s Mike Ryan cautioned that changes in human behavior are still the major driving force for the resurgence. “It’s too easy to just lay the blame on the variants and say it’s the virus that did it,” he said. “Unfortunately, it’s also what we didn’t do that did it.”
However even if the variant plays a crucial role it might be driving the boost because it is transmitted more easily, like B.1.1.7, not because it can evade the immune response. “Of course it could be a combination of these factors, too,” Dr Pybus says. Similarly, in a recent modeling study, researchers at the London School of Hygiene & Tropical Medicine calculated that South Africa’s 501Y.V2 variant could be 50% more transmissible but no better at evading immunity or just as transmissible as previous variants but able to evade immunity in one in five people previously infected. “Reality may lie between these extremes,” the researchers wrote.
Dr Ester Sabino, a molecular biologist at the University of São Paulo, São Paulo, is launching a study to find reinfections in Manaus that could help decide between these hypotheses for P.1. She is also working to sequence more samples from Manaus from January to follow the variant’s spread. “We don’t have the data yet, but my guess is, it will be at 100% now,” she says. Lab studies investigating the variants are also underway.
Meanwhile the United Kingdom launched a new consortium, G2P-UK (for “genotype to phenotype-UK”), headed by Wendy Barclay of Imperial College London, to study the effects of emerging mutations in SARS-CoV-2. One idea discussed at the 12 January WHO meeting is to set up a biobank that would aid studies by housing virus samples, as well as plasma from vaccine recipients and recovered patients. https://www.ukri.org/news/national-consortium-to-study-threats-of-new-sars-cov-2-variants/
It should be noted that interactions between the new mutations may make it harder to tease out their effects. The variants from the United Kingdom, South Africa, and Manaus all share a mutation named N501Y, for instance, or Nelly, as some researchers call it.
However the mutation, which affects the spike protein, also occurs in some variants that do not spread faster, suggesting N501Y does not operate alone, says Dr Kristian Andersen of Scripps Research: “Nelly might be innocent, except maybe when she’s hanging with her bad friends.”
There are also new variants being discovered in the United States (not just the variants discovered in Ohio but newer variants discovered in other states!) and also in India that has yet to be presented to the media yet. Thailand Medical news will be providing first exclusive stories on these.
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