JN.1 is Canada’s new dominant COVID-19 subvariant. Here’s what to know

A new COVID-19 subvariant, known as JN.1, has emerged and is now the prevailing strain across Canada, prompting health experts to caution that it may be more infectious and could even have extra symptoms.

Currently, the subvariant makes up the highest proportion of all COVID-19 variants, accounting for more than half (51. 9 per cent) of all infections in Canada, according to the latest data from the Public Health Agency of Canada (PHAC).

JN.1 was first detected in Canada on Oct. 9, and since then has rapidly increased.

“If this virus continues to circulate at high levels, that means more virus, which means more mutations and more evolution, which means more of this same kind of issue happening repeatedly,” warned Ryan Gregory, a professor of integrative biology at the University of Guelph, and evolutionary biologist.

1:54 Low vaccine uptake fuels spike in respiratory illnesses: health officials

On Dec. 10, the JN.1 subvariant made up 26.6 per cent of all COVID-19 variants in Canada, but was not the dominant strain. At that time, HV.1 still made up 29 per cent of all subvariants, according to PHAC data. By Dec. 17, JN.1 made up the highest percentage (38.5 per cent) of all subvariants across Canada. Meanwhile, HV.1 fell to 24.4 per cent.

The World Health Organization (WHO) on Dec. 19 added JN.1 to its list of variants of interest, its second-highest level of monitoring. Despite the categorization, the health organization said JN.1 poses a low additional public health risk.

Two days later, on Dec. 21, PHAC labelled it as a variant of interest in Canada.

As the subvariant continues to circulate, here is what we know so far about JN.1.

The JN.1 subvariant is a sublineage of BA.2.86 that emerged in Europe in late August 2023. It is another Omicron variant, according to PHAC. Gregory explained that JN.1 is a “grandchild” of BA.2.86. The original BA.2.86 probably evolved within a single person with a long-term infection over a year, he added.

“So, somebody was infected. The virus continued to replicate and change within their body and then it reentered the rest of the population,” he said. “Once it gets back into the main population, it’s now evolving at the level of among hosts.”

This in turn created the more competitive and successful JN.1. It featured a single alteration in the spike protein, enhancing its ability to effectively bind to cells, according to Gregory.

6:14 Holiday health update: Navigating the flu, RSV and COVID

“It has massively managed to compete with the existing things that were out there, which suggests that it’s either very good at transmitting, and escapes immunity that is otherwise conferred by prior infection or previous vaccination,” he said. “So in other words, it’s different enough that your immune system, having been trained on older variants, doesn’t recognize it as well.”

He also believes JN.1 may be the starting point for subsequent evolutions, much like the XBB variant. The XBB variant, another sublineage of Omicron, started circulating the world in late 2022. In 2023, some of its descendents, such as XBB.1.5 and EG.5, became dominating COVID-19 infections.

It is currently not known whether JN.1 infections produce different symptoms from other variants, health experts say.

The typical symptoms of COVID-19 according to the government are:

• Fever or chills
• Cough
• Shortness of breath
• Fatigue
• Muscle or body aches
• Headache
• Sore throat
• Runny nose

Additionally, Gerald Evans, an infectious disease specialist at Queen’s University in Kingston, Ont., said he has heard more people report gastrointestinal (GI) issues, such as diarrhea.

“The one thing I have been hearing about, they have GI symptoms, and these are not new, these have been recorded since COVID came out,” he said. “But anecdotally, the number of people having GI symptoms seems to be slightly higher, but you have to be careful with that because it’s an observational bias. But it does strike me that it’s becoming a bit more of a theme in the last month.”

Gregory agreed with this observation but added that it may still be too early to tell if this is a hallmark symptom of the JN.1 variant.

He added that it is difficult to determine which symptoms go with what variant, especially when so many are circulating and there is less testing for COVID-19.

Due to JN.1’s fast growth, experts like Gregory say it’s either more transmissible or better at evading our immune systems. However, PHAC said in an email to Global News on Dec. 19, there is no evidence of increased severity associated with this variant.

The WHO also stated last month that it is anticipated that this variant may cause an increase in COVID-19 cases amid a surge of infections of other viral and bacterial infections, especially in countries entering the winter season.

Since the spike protein is also the part that existing vaccines target, current vaccines should work against JN.1 and other lineages of BA.2.86, explained Evans. Preliminary evidence shows that protection by the XBB recombinant vaccine also guards against JN.1, he added. However, he cautioned, “If it has been a year since your last vaccine or COVID infection, you may be more susceptible.”

Personal protective measures are effective actions to help reduce the spread of COVID-19, PHAC stated. They include things like staying home when sick, properly wearing a well-fitted respirator or mask, improving indoor ventilation and practicing respiratory etiquette and hand hygiene.

“These measures are most effective when layered together,” PHAC stated in an email.

Laboratory studies also suggest that the current therapeutic antiviral options, such as Paxlovid, available in Canada are expected to be effective against SARS-CoV-2 sub-lineages, PHAC added.

In some parts of the country, COVID-19 cases have been steadily increasing since the fall, yet the numbers appear to be stable now, according to Evans. However, while infection numbers remain stable, they are still “very high and very steep,” he warned, well beyond influenza, RSV and all the other viruses.

4:50 Kingston pharmacist urging residents to get vaccinated to avoid getting sick this winter season

He believes there may have been a holiday spike in COVID0-19 infections for several reasons, but most importantly noting that the uptake COVID-19 vaccine has “been very poor.”

As of Dec. 8, PHAC reported that 14.6 per cent of eligible Canadians have received the updated vaccines targeting XBB.1.5.

“The second reason, of course, is we’re in the middle of the respiratory virus season,” Evans said. “And although there are still a fair percentage of people who are being careful, there are a lot of people really have just gone back to what life was like before 2020. And. That’s, of course, a moment of opportunity for all these viruses to kind of take off.”