South African COVID-19 variants found in Hawaii

The omicron variants BA.4 and BA.5, currently the dominant lineages of the coronavirus circulating in South Africa, have recently been detected in Hawaii, according to the state Department of Health.

DOH’s latest variant report, published Wednesday, confirmed one case of BA.4 and one case of BA.5 detected through whole genome sequencing in samples in May.

There is no reference to which county the case of BA.4 was detected in. The case of BA.5 was detected in a specimen from Hawaii island. Both BA.4 and BA.5 contain four additional mutations within the spike protein when compared with BA.2, and are estimated to be about 1.6 and 1.8 times more transmissible, respectively, than BA.2, according to the report.

In May the European Centre for Disease Prevention and Control reclassified BA.4 and BA.5 as variants of concern, noting no indication of increased severity over previous variants, but that they appear to be more transmissible.

The European agency encouraged countries to remain vigilant for signals of BA.4 and BA.5 emergence through testing and surveillance.

The United Kingdom Health Security Agency has also elevated BA.4 and BA.5 to variants of concern on the basis of observed growth, according to a recent news release.

“Whilst Omicron BA.4 and BA.5 are in the early stages of growth in the UK, analysis of the available data suggests that they are likely to have a growth advantage over the currently-dominant Omicron BA.2 variant,” said UKHSA in the release. “There can be several reasons for growth advantage, but in the case of BA.4 and BA.5, laboratory data suggests a degree of immune escape which is likely to contribute.”

Marie Van Kerkhove, COVID-19 technical lead for the World Health Organization, said Thursday it is tracking sublineages BA.4 and BA.5 with the help of researchers in South Africa.

During a livestreamed Q&A session, she said it appears that South Africa’s surge of BA.4 and BA.5 has peaked and is now declining.

“But their hospitalizations have remained quite low, and that’s a good sign,” she said, “because we were worried about a potential change in severity, which we are not seeing with BA.4, BA.5.”

She urged countries to keep up testing and surveillance in order to track evolutions of the coronavirus.

BA.2 still makes up the largest proportion of variants circulating in Hawaii, at 70%, according to the report, while its descendant BA.2.12.1 now makes up 29%, about double what was reported two weeks ago.

Eight cases of omicron subvariant XE — which contains genetic material from BA.1 and BA.2 — have now been detected in Hawaii as well. Six of them were detected in Honolulu.

DOH’s State Laboratories Division conducts viral genome sequencing on a fraction of positive specimens collected every week, and generates a variant report every two weeks.