Genome sequencing reveals COVID-19 mutated in Waikato immunocompromised case 11 times

Scientists have spelt out another reason why it's so important to protect the immunocompromised from COVID.

It's because they can suffer from what’s known as “persistent infection” and become a breeding ground for new variants.

Official Information obtained by Newshub shows one immunocompromised patient returned a positive result in four separate tests since February, and genome sequencing showed the virus had mutated 11 times in that person.

It comes as experts say the most transmissible variant yet, BA-5, is expected to dominate community cases within weeks. 

Despite this, at Westfield Mall in Auckland’s St Lukes on Thursday, it quickly became apparent many shoppers were not concerned with the orange setting rules when it came to mask-wearing. 

Even in the presence of signs which reminded them of their obligations, some didn’t bother wearing masks.

"It is a really important way of making sure that transmission of COVID and influenza is reduced," said COVID-19 Response Minister Dr Ayesha Verrall. 

Under the orange setting, it's not just important, it's a requirement in places like malls. But tolerance for rules is waning.

Newshub spent eight minutes at St Lukes Mall, and in that time, we counted more than a dozen people who were not wearing masks.

And masks and boosters are even more important right now according to senior lecturer at the Centre for Computational Evolution at Auckland University Dr David Welch, who's helping track the virus. 

"Cases are starting to increase and it looks like we're at the beginning of a new wave."

On Tuesday the number of cases hit just over 8000, with 16 deaths, followed by a slight dip yesterday, and today another 7000 odd cases and 19 deaths.

Genome sequencing reveals COVID-19 mutated in Waikato immunocompromised case 11 times

The more transmissible variant BA.5 is quickly getting established. 

"I think we're heading for BA.5 becoming the dominant variant by early to mid-July, so just a couple of weeks away," said Dr Welch. 

ESR wastewater tests show three weeks ago, BA.5 accounted for 2.8 percent of infections. 

It doubled to 6 percent two weeks ago, and this week it almost doubled again to 10.5 percent. 

And BA.5 has a distinct advantage over the current dominant variant, known as BA.2.

"Somewhere in the ballpark of 40 to 50 percent more transmissible than BA.2," Dr Welch said. 

The rise of BA.5 is expected to put further pressure on already overburdened hospitals and doctor's clinics. 

"The pressure is very significant at the moment. It's probably one of the worst winters we have seen. We have influenza, COVID and possible upswing of COVID starting to occur," said Royal College of GPS Medical director Dr Bryan Betty.

Official Information reveals how effective the virus is at evolving if given the right environment. 

An ESR report details the case of an immuno-compromised Hamilton case, who suffered what's known as persistent infection. 

It means they could not get rid of the virus. They tested positive on four separate tests since the end of February.

And a genome sequence revealed the virus had managed to mutate 11 times while infecting the individual. 

ESR has systems in place to monitor the COVID-infected immunocompromised and there's a good reason. 

Dr Welch said persistent infection can last for "many months" and it can become "an ideal breeding ground" for new variants.

At the other end of the spectrum, there are reinfections. More variants mean it'll be easier for anyone to get the virus again, even just a month after getting it the first time.

"There's a small risk of reinfection after 29 days, and we're now reflecting that in our guidance," said Minister Verrall. 

That advice is if you have symptoms 29 days after first getting the virus, test. And if you're positive, you'll need to isolate yourself again for seven days.

Minister Verrall said Thursday the last time New Zealand entered the red traffic light setting was when the country had over 10,000 cases a day. 

Dr Welch says we’re not far off that currently. 

The Government announced today a number of measures to help counter the virus spread. It’s funding child-sized masks for schools and will help pay for schools' heating bills to encourage teachers to open doors and windows to help ventilate classrooms.