Random variation is an essential component of all living things. It drives diversity, and it is why there are so many different species. Viruses are no exception. Most viruses are experts at changing genomes to adapt to their environment. We now have evidence that the virus that causes Covid, SARS-CoV-2, not only changes, but changes in ways that are significant. This is the nineteenth part of a series of articles on how the virus changes and what that means for humanity. Read the rest: part onepart twopart threepart fourpart fivepart sixpart sevenpart eightpart ninepart ten,part elevenpart twelvepart thirteenpart fourteenpart fifteenpart sixteenpart seventeen, and part eighteen.

As the scientific community becomes keenly aware of the dangers SARS-CoV-2 variants present, increased sequencing efforts seek to uncover new mutants before they begin to spread widely in the population. Among the new variants discovered in recent weeks is the Japanese variant (B.1.1.248) identified both through spread in the community and in their Covid-19 isolation facility. This viral mutant is nearly identical to the Brazilian (P.1) variant and carries similar mutations to the infamous United Kingdom (B.1.1.7) and South Africa (B.1.351), but also has one mutation unique to its structure, further complicating the Covid-19 puzzle for Japan and the world.

In early January, The National Institue of Infectious Diseases in Japan detected a new variant of SARS-CoV-2 in travelers arriving from Brazil a few days earlier. The new variant carried identical mutations to the spike protein as P.1, aside from one additional point mutation—V1176F. Notably, B.1.1.248 carries the N501Y mutation, which is documented to increase the virus’s transmissibility, and E484K, which increases the virus’s resistance to neutralizing antibodies. Mutations to other proteins were not included in the published literature.


P.1 is a particularly nasty variant of SARS-CoV-2. It has reinfected people in Manaus, making them sick once again after infection earlier in the pandemic. It is also highly transmissible and reportedly resistant to antibodies from both vaccines and monoclonal antibody therapies.

The unique point mutation V1176F is located in the second heptad repeat of the virus. The heptad repeats form a helix structure centrally-located on the virus. These helical bundles are essential for the viral fusion of the virus to the human cell. A mutation to this region may increase the transmissibility of the virus by optimizing viral fusion, but further investigation is necessary to confirm this hypothesis.

The six-helix structure formed by HR1 and HR2 of the S2 subunit.
The six-helix structure formed by HR1 and HR2 of the S2 subunit. YUAN HUANG ET. AL // APS
Schematic representation of the SARS-CoV-2 spike.
Schematic representation of the SARS-CoV-2 spike. YUAN HUANG ET. AL // APS

Japan’s Covid-19 timeline mirrors that of the United States. In April and July, there were spikes in infections. Late October through mid-January saw an explosion in cases, peaking around January 9th. Recent weeks have brought about much lower infection rates as the third wave has seemingly passed, but a new, more transmissible and antibody-resistant variant could complicate progression.

The new variant has been detected in 93 cases throughout the country, according to Chief Cabinet Secretary Katsunobu Kato, but that number is likely higher due to unreported cases. Ideally, these cases would be isolated to prevent further spread, but only time will tell if B.1.1.248 creates more significant inroads in the country.

B.1.1.248 is but a short entry in a more extensive Covid-19 anthology. As we continue vaccination efforts worldwide, variants potentially resistant to vaccines are appearing in tandem, including the Japanese variant. B.1.351 has even recently been detected in the United States. Not to mention, there may be other point mutations that have similar or greater effects on antibody resistance yet to emerge.

In the past month, many countries have seen a deep decline in Covid-19 cases, like the United States and the United Kingdom, but elsewhere cases have plateaued or even slightly risen, like in India, likely due to these new variants. Whether a repercussion of vaccinations, increased natural immunity, luck, or a combination of these, we mustn’t falter in our Covid-19 prevention efforts. These variants present a great risk. 

As the influenza virus returns every year with a different strain, the same could be said for SARS-CoV-2. Antibodies developed from natural infection or administered via vaccine will not last forever. As they decay, the virus will find ways around our immune defenses. The front line of defense has to remain public health measures. Social distancing, contact tracing, and isolation must continue as the stalwart protections against a potential new wave.