In South Africa, 16 new lineages of SARS-CoV-2 were isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere.
B.1.1.54, B.1.1.56 and C.1 spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G, was the most widespread lineage in South Africa by the end of August 2020.
An early South African-specific lineage, B.1.106, which was identified in April 2020, became extinct after nosocomial outbreaks were contained.
Then in December 2020, the 501Y.V2 variant was noticed. This has acquired 23 mutations, when compared with the original Wuhan virus. Importantly, 20 of the mutations cause amino acids changes and eight are located in the spike protein itself.
Within a short time the 501Y.V2 became the dominant variant in SA with around 80% of the cases. What's alarming is that 501Y.V2 may escape antibodies generated from previous infection. This means that antibodies from people who were infected with previous variants may not work as well against 501Y.V2. Also this will affect the vaccines.
Some recent trials in SA, shows that the efficacy of the Oxford vaccine can be low as 10% for this variant.
But also note that the sample sizes for these results are small and the figures might not be that accurate.
In Brazil another variant emerged known as P.1. This variant has 17 unique mutations, including three in the receptor binding domain of the spike protein. This variant was detected in the US at the end of January 2021, being first detected at Haneda Airport in Japan on routine screening in those arriving from Brazil. This variant dominates in the Amazonias.
Here's brief comparison on current variants of interest. The vaccine developers will modify their vaccines to handle the variants. But it will take some time. Who knows what will happen in the future. Viruses mutate all the time and no one can predict the changes.
B.1.1.54, B.1.1.56 and C.1 spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G, was the most widespread lineage in South Africa by the end of August 2020.
An early South African-specific lineage, B.1.106, which was identified in April 2020, became extinct after nosocomial outbreaks were contained.
Then in December 2020, the 501Y.V2 variant was noticed. This has acquired 23 mutations, when compared with the original Wuhan virus. Importantly, 20 of the mutations cause amino acids changes and eight are located in the spike protein itself.
Within a short time the 501Y.V2 became the dominant variant in SA with around 80% of the cases. What's alarming is that 501Y.V2 may escape antibodies generated from previous infection. This means that antibodies from people who were infected with previous variants may not work as well against 501Y.V2. Also this will affect the vaccines.
Some recent trials in SA, shows that the efficacy of the Oxford vaccine can be low as 10% for this variant.
But also note that the sample sizes for these results are small and the figures might not be that accurate.In Brazil another variant emerged known as P.1. This variant has 17 unique mutations, including three in the receptor binding domain of the spike protein. This variant was detected in the US at the end of January 2021, being first detected at Haneda Airport in Japan on routine screening in those arriving from Brazil. This variant dominates in the Amazonias.
Here's brief comparison on current variants of interest. The vaccine developers will modify their vaccines to handle the variants. But it will take some time. Who knows what will happen in the future. Viruses mutate all the time and no one can predict the changes.
| B.1.1.7, 20I/501Y.V1 | Late Dec UK now spread over 62 countries | 17 recent mutations, including N501Y, P681H, HV 69–70 deletion, and four on the spike protein; the ORF8 Q27stop mutation outside the spike protein | Increased transmissibility & virulence (not proven) - current vaccines little concern. Both Pfizer & BioNTech reported their current vaccines are effective. |
| B.1.351, 20C/501Y.V2 | Late Dec South Africa - now detected in EU & Asia | 21 mutations, including N501Y, E484K, and K417N on the spike protein, and ORF1b deletion outside the spike protein | Increased transmissibilty (suggested) Worry about the efficacy of current vaccines. In-vitro sera studies show that the mRNA vaccines are only impacted slightly. |
| P.1, 20J/501Y.V3 | Brazilian variant | 17 amino acid changes, including N501Y, E484K, and K417N on the spike protein; ORF1b deletion outside the spike protein | Multiple re-infections. Immune evasion under study and yet unresolved. |
| COH.20G/501Y | Few cases in the US | N501Y, in the virus’ spike protein. It lacks most other mutations present in the B.1.1.7 variant identified in the UK. | Behaviour reported to be not much different to the original virus. |
| S Q677H | Dec 2020 & Jan 2021 some parts in US | Q677H mutation on the spike protein, A85S on the M protein, and D377Y on the nucleocapsid protein | Behaviour reported to be not much different to the original virus. |
| L452R, B1429 | First in the UK and Europe - later in the US | L452R mutation, on the spike protein | Reported in several large outbreaks. Vaccine efficacy still under investigation |
