Avian Flu Diary: Japan: NIID Reporting A New COVID Variant Detected In 4 Travelers From Brazil

VARIANT COMPARISON - Credit Japan's NIID

#15,699

While we've been primarily focused on the highly transmissible B.1.1.7 COVID variant first reported in the UK, and the 501Y.V2 variant - which carries the E484K mutation - which is raging in South Africa, these aren't the only VOC (variants of concern) we've been watching.

Four days ago, in Argentina: PAIS Report On COVID E484K Variant In South America, we looked at the first report of another variant - with some of the same mutations as the B.1.1.7 and 501Y.V2 variants - found circulating in Argentina.

A similar variant had been reported previously in Brazil, and three days ago, in PrePrint: Genomic Evidence of a Sars-Cov-2 Reinfection Case With E484K Spike Mutation in Brazil, we looked at a recent reinfection with this variant.

While the characteristics of these two variants remain largely unknown, they both carry mutations that appear to have conveyed significant evolutionary advantages to other variants.

Given the limits of surveillance and genomic sequencing, how widespread they already are - and their rate of growth - are also unknown.

Today, the plot thickens with the announcement from Japan's National Institute of Infectious Diseases (NIID) of the recent detection of a new COVID variant - sharing some (but not all) of the same mutations as those variants described above - in 4 recent arrivals from Brazil.

While details remain scant, we have this link and (translated) excerpts from today's announcement:

(Translated)

New mutant strain of new coronavirus detected in returnees from Brazil

PUBLISHED: JANUARY 10, 2021

National Institute of Infectious Diseases
January 10, 2021

PDF version

WRAP UP
New mutants have been detected in returnees from Brazil that share some of the mutations in common with those of concern for increased infectivity.
The mutant strain is limited to information on gene sequences, and it is difficult to determine infectivity, pathogenicity, effects on testing methods and vaccines, etc. at this time.
It is desirable to keep the infected person of the mutant strain under control in a private room and to carry out an active epidemiological survey including the source of infection, tracking and management of close contacts, clinical course, etc.
Even for mutant strains, as in the past, it is recommended that individuals' basic infection prevention measures include avoiding three-cs, wearing a mask, and washing their hands.
Text
On January 6, 2021, the National Institute of Infectious Diseases detected a new mutant strain of the new coronavirus in four travelers arriving from Brazil on January 2.
The novel mutant belongs to the B.1.1.248 strain * 1 and has 12 mutations in the spike protein * 2 . Similar to VOC-202012 / 01 and 501Y.V2 of mutant strains that are concerned about increased infectivity , N501Y mutation is observed at the receptor binding site * 3 of peplomer protein, and E484K mutation is observed like 501Y.V2.
Mutations in E484 have been reported as escape mutations * 5 from monoclonal antibodies * 4 that neutralize SARS-CoV-2 (1,2). Furthermore, experimental data (3) that the E484K mutation was found in the escape mutant strain * 6 from the recoverer plasma, and the mutation of E484 reduced the neutralizing antibody titer of the pseudotype virus * 7 in the recoverer plasma by about 10 times. (4) reports that it is difficult to suppress viral cell infection in vitro ( in vitro ) even in the presence of anti-SARS-CoV-2 antibody induced in the serum of COVID-19 recoverers. Has been done. That is, there is a concern that the conventional immunity against the virus may be diminished against the virus having the E484 mutation.
In Brazil, there are reports of reinfection cases with mutant strains showing the E484K mutation of the B.1.1.248 strain (2021/01/06) (5), but they are not the same as the novel mutant strain.
The mutant strain is limited to information on gene sequences. At present, it is difficult to determine the infectivity and pathogenicity in humans, the effects on testing methods, the effects on vaccines, etc., and further investigation is required.
It is desirable that the infected person of the mutant strain be kept under the control of a private room and actively conduct an epidemiological survey including the source of infection, follow-up and management of close contacts, and clinical course.+
Even for mutant strains, as in the past, it is recommended that individuals' basic infection prevention measures include avoiding three-cs, wearing a mask, and washing their hands.