Fiocruz Genomic Network identifies the appearance of a new Omicron variant

Last Saturday (November 12) the Fiocruz Genomic Network announced the appearance of a new Omicron variant in the state of Amazonas. The variant seems to be responsible for the recent increase in the number of cases in the state. According to researcherTiago Gräf, of the Genomic Network, Amazonas has been a sentinel territory for COVID-19 monitoring. “What happens in the state tends to also happen in other regions, and it may be happening again”. This new variant is called BE.9. The description of yet another variant by the Fiocruz Genomic Network underscores the importance of having researchers continue to sequence Sars-CoV-2 and study its evolution.

BE.9 is the same underline BA.5.3.1, that is, it is an Ômicron of lineage BA.5 (Photo: Camila Boehm/Agência Brasil)

Gräf, who analyzed the results found by the team led by virologist Felipe Naveca, of Fiocruz Amazônia, mentioned that COVID-19 cases in Amazonas had been rising since mid-October, and have spiked from a moveable average of about 230 cases per week to about 1,000. To investigate what may be causing this reappearance of COVID-19 in the state, Naveca’s steam sequenced more than 200 Sars-CoV-2 genomes in September and October, therefore identifying the new variant.

Naveca highlights that one of the factors that facilitates the identification of new variants is the fact that Amazonas has the largest Sars-Cov-2 sequencing coverage in Brazil, as a function of the number of confirmed cases, the measure used by the WHO. “As we carry out surveillance in a large percentage of cases, working in a partnership with the state’s Foundation for Surveillance in Health, and with LACEN/AM, we are able to make these identifications early and to explain how the variants appear”, he explains.

BE.9 is an evolution of sub-lineage BA.5.3.1, which is an Omicron variant of lineage BA.5. Naveca states that because of the mutations found in BA.5.3.1 of Amazonas, the committee in charge of classifying lineages (PANGOLIN, in the United Kingdom) has been asked to create a designation specifically for this sub-lineage, now officially called BE.9. According to Naveca, the two sub variants (BQ.1 and BE.9) share some of the same mutations, but both seem not to cause an increase in the number of severe cases, at least up to this moment.

“What we have been intrigued about with this new variant is that it has mutations K444T and N460K in the spike, exactly like BQ.1.1. BE.9 also has a deletion in the spike, in position YKK”, says Gräf. According to the researcher, “The BQ.1.1 variant descends from BE.1, which also descends from BA.5.3.1. This means that BA.5.3.1 has generated lineages with the same spike mutations in different places of the world, and independently. In evolutionary studies, we call this ‘convergence’”.

According to Gräf, “BE.9 and BQ.1.1 have their differences in other regions of the genome, but they are very similar in the spike. This is why it’s very important that we keep a close eye on BE.9, as we’ve already seen that it has made COVID-19 reappear in Amazonas and we don’t know whether it can do the same in the rest of Brazil”. The researcher believes there will be a competition among these “cousin” variants in other states. “The BQ.1.1 has already been identified in São Paulo, Santa Catarina, Pernambuco and Rio de Janeiro, and it’s possible that it’s already present in other states. We don’t know about BE.9 yet, as its lineage designation took place on November 12. After this date we’ll be able to monitor it better”.

However, Gräf, as Naveca, remains optimistic, as the number of cases of SARS and deaths by COVID-19 do not seem to be increasing significantly due to BQ1.1 (according to international data), nor to BE.9. “In Amazonas, for instance, in spite of the number of cases, this wave caused by the BE.9 is smaller than the one caused by the BA.5 and much smaller than the BA.1 wave. The same can be observed for hospitalizations due to SARS. In the state of Amazonas, the BE.9 wave seems to have already reached its peak, and is expected to begin falling soon”, said Gräf.