Coronavirus: BA.2 Omicron cases outnumber BA.1 in New Zealand, Delta infections still occuring

The BA.2 sublineage of Omicron is now outnumbering cases of the variant's original strain BA.1 in New Zealand.

BA.2 is described by New Scientist as "another flavour" of Omicron that has been around from the start. The term Omicron is used to describe a family of variants that appeared in Botswana and South Africa in November.

BA.2 has 32 of the same mutations as BA.1, but it also has 28 that are different, New Scientist says.

Professor Mike Bunce and Dr Joep de Ligt, both from the Institute of Environmental Science and Research (ESR), say the interplay of BA.1 and BA.2 lineages is one of the key pieces of data that they are monitoring across New Zealand.

"For the first time this week BA.2 cases outnumbered BA.1 in our sequenced genomes. This was expected as BA.2 appears to have a transmission advantage over BA.1," they say.

"With less stringent border restrictions we expect to see new lineages of viral genomes - genomics enables us to watch these closely. We are also keeping an eye out for Delta cases, although they are becoming hard to spot within the Omicron wave."

Although Omicron cases make up the majority of infections in New Zealand, Director of Public Health Dr Caroline McElnay says there are still Delta cases circulating.

"[ESR] were seeing the occasional Delta, but it had actually been some days since they'd seen a case that was whole genome sequenced as Delta," she told reporters on Tuesday.

"Our whole genome sequencing is the only way we can distinguish between Delta and Omicron, and at the moment because of the sheer number of cases, we're not able to whole genome sequence all of those cases. 

"So there's a prioritisation process in place for that whole genome sequencing, and that is very much focused on our hospitalised cases."

Since not all cases are being whole genome sequenced, Dr McElnay says there may be some Delta infections in the community that haven't been picked up.

Dr Caroline McElnay.
Dr Caroline McElnay. Photo credit: Getty Images

New Zealand reported a record 23,894 COVID-19 cases on Tuesday, with 757 people in hospital.

The Ministry of Health said that as the Omicron outbreak continues, they're continuing to see a larger proportion of unvaccinated cases in hospitals with COVID-19.

"Just 3 percent of eligible people aged 12 and over in New Zealand have had no doses of the vaccine. However, of those aged over 12 in Northland and Auckland hospitals with COVID-19 for whom we have vaccination data recorded, 19.4 percent have had no doses of the vaccine," they say.

"Even early in the Omicron outbreak, the figures show that, based on the data available, unvaccinated people are significantly over-represented in the current hospitalisation data.

"The numbers send a clear message: getting vaccinated will help to keep you out of hospital if you catch COVID-19 and could save your life."