New Coronavirus News from 18 Nov 2022

Human case of swine-origin influenza A virus detected in Denmark, according to CDC study [News-Medical.Net, 18 Nov 2022]

By Neha Mathur

In a recent study published in the Emerging Infectious Disease Journal, researchers detected a swine influenza A virus (IAV)-infected patient in routine surveillance at the National Influenza Center in Denmark. The detected influenza variant appeared distinct from any variant found previously in Denmark.

Background
As per official records, during the 2021–22 influenza season, 16,160 cases in Denmark were due to the influenza A virus, predominantly the H3N2 subtype. During this time, no cases of swine-origin influenza virus occurred in humans. Since the 2009 influenza A(H1N1) pandemic, no reports of persistent human-to-human IAVs transmission have come to light. Also, there have been only sporadic reports of human infections with swine IAVs. Yet, the zoonotic potential of IAVs is highly concerning.

Case report
A young man in his 50s, working at a swine abattoir in Denmark, was hospitalized after acute onset of illness on November 24, 2021. He had dizziness in the night, followed by chest pain, pain radiating toward the left arm, diarrhea, and malaise, but no fever. The patient suffered repeated convulsions and had to be admitted to the intensive care unit (ICU) and put on ventilation to cease seizures and manage declining oxygen levels.

He had no cardiovascular, kidney, neurological, or other impairment, including pneumonia, that could rationalize his sudden bout of severe illness. However, a pharynx swab sample of the patient tested positive for IAV. Notably, no other coworker at the patient's workplace reported the incidence of influenza.

With antiviral medication (oseltamivir) and supportive treatments, the patient's clinical condition improved over the next two days, so he was discharged from the hospital. The researchers submitted the remaining sample material to the Danish National Influenza Center, which confirmed it was positive for the pandemic H1N1 strain.

Further analysis by whole-genome sequencing revealed its consensus sequence to be of the H1N1 subtype. Notably, the virus was more similar to swine IAVs than human influenza strains. The team uploaded this sequence to the global initiative on sharing all influenza data (GISAID) database.

The sequence had no match to IAV sequences in GISAID, as revealed by the Basic Local Alignment Search Tool (BLAST) searches; however, a comparison to in-house sequences of swine influenza viruses from Denmark showed a close resemblance to 2021 swine IAVs. This viral strain had several genetic and antigenic differences from other influenza A viruses detected in Denmark. Also, it had poor reactogenicity to the currently used human seasonal influenza vaccines. Furthermore, its phylogenetic analyses revealed that most gene segments were similar to the H1N1 subtype. On the contrary, its neuraminidase and non-structural segments belonged to the clade 1C avian-like swine influenza A(H1N1) found in Eurasia.

Conclusion
Earlier in Denmark, an elderly patient with comorbidities experienced classical influenza-like illness (ILI). However, the reported case in this study was unique because a previously healthy adult experienced severe and sudden illness. Another distinct observation was that this patient experienced convulsions, which are rare in adults and typically accompanied by fever or encephalitis. Therefore, the infecting viral strains in these two cases are likely genetically distinct.

Detection of a variant IAV via routine surveillance highlighted the importance of continuous monitoring of both human and swine IAVs with zoonotic potential. Additionally, it underscored the need to promptly take countermeasures for those who come in contact with swine owing to their occupation and experience ILI.

Journal reference:
• Andersen KM, Vestergaard LS, Nissen JN, George SJ, Ryt-Hansen P, Hjulsager CK, et al. (2022). Severe human case of zoonotic infection with swine-origin influenza A virus, Denmark, 2021. Emerging Infectious Diseases. doi: https://doi.org/10.3201/eid2812.220935 https://wwwnc.cdc.gov/eid/article/28/12/22-0935_article

What does the COVID-19 'variant soup' mean for the Asia-Pacific region as travel ramps up? [ABC News, 18 Nov 2022]

By Erin Handley

As Australia anticipates a fourth wave the Asia-Pacific region has been served up what is been dubbed a "COVID variant soup".

Key points:
• New COVID variants are competing for dominance in the region
• Singapore recently had a rise in hospitalisations due to XBB
• Countries like Japan and South Korea are bracing for a "twindemic" of COVID and flu in winter

This soup is a mix of sub-variants vying for dominance according to Sanjaya Senanayake from the Australian National University Medical School.

"It's all still Omicron, but it's these new sub-variants. So they're going to challenge our immune system, and we will see an increase in cases," Dr Senanayake said.

"But hopefully, because of our hybrid immunity, it should be a short, sharp wave in terms of both cases and hospitalisations."

The COVID variant "swarm" or soup adds a complexity that makes waves harder to predict, according to the science journal Nature.

The current state of the virus is varied across our region; as Singapore comes down from the crest of a wave fuelled by the variant XXB, Japan is seeing an uptick in cases.

Case numbers appear to be fairly stable in South-East Asian countries, where many Australians might travel over the upcoming holiday period.

Meanwhile, many Pacific countries are reporting low or no COVID cases despite experts saying transmission is still occurring, highlighting that the quality of data collection varies drastically between nations.

Global health researcher at the University of Sydney School of Public Health Meru Sheel said it's no longer fruitful to draw comparisons at this stage.

"We're definitely way past that phase of the pandemic where we should be comparing countries … I think it's arbitrary," Dr Sheel said.

"The borders are open, people are moving, viruses are circulating … whether we like it or not, infection is inevitable."

Still, there are some lessons to be learned from outbreaks abroad.

And there are measures people can take to protect themselves and their communities, which can also have an impact at a population level.

Winter is coming in Japan
Australia is bracing for a fourth COVID wave, but Japan is looking at its eighth.

The Japanese health ministry's experts panel warned it could be the biggest surge in case numbers for the country since the pandemic began.

Last month Japan lifted travel restrictions for foreigners welcoming almost half a million overseas travellers in October — more than double the previous month.

It is also entering winter, like other northern-hemisphere countries South Korea and Taiwan — although for now Taiwan's cases are declining.

Dr Senanayake said COVID was perennial but can pose more of a problem in winter, in part due to behavioural reasons – such as people gathering together closely indoors to escape the cold.

"They also have to worry about the 'twindemic' with the flu resurgence, as we saw in Australia," he said.

The twindemic is something nearby South Korea is expecting too, according to Kim Woo-joo, a professor of infectious diseases at the Korea University Guro Hospital and one of the country's leading COVID experts.

"From late October, the daily number of newly confirmed COVID-19 cases are increasing," Dr Kim said.

The resurgence has several causes; the proliferation of sub-variants from abroad, mass gatherings for events and the easing of restrictions, although indoor mask-wearing is still required and a seven-day isolation period is still recommended.

"Government does not want to enforce social distancing measures anymore," Dr Kim said.

There is also some degree of complacency from individuals, as well as low vaccination rates for the fourth dose and Omicron bivalent vaccines, he said.

"Increasing vaccination rates among people is necessary, but the acceptance rate is very low, even compared to that of the United States."

Cases are climbing and Dr Kim said he expected an increasing wave, with BQ.1 and BQ.1.1 emerging as the dominant sub-variants.

Singapore's 'short, sharp' XBB wave
The BQ.1 offshoots are also expected to lead to rising infections in Europe, North America and Africa, but it was a different story in Singapore recently.

The city-state is seeing a decline after a spike in cases and hospitalisations fuelled by the highly-transmissible XBB variant.

"XBB is what we call a recombinant strain, so it's two different COVID strains or sub-variants coming together," Dr Senanayake said.

"But the good news is that Singapore had a short, sharp rise in cases – it wasn't anything as bad as their worst peak by any means.

"And it started to come down very quickly, both in terms of cases and hospitalisations."

Both BQ.1 and XBB are present in Australia and could become dominant here.

Singapore is one of the busiest aviation hubs in Asia, which could aid its spread.

Although Singapore saw an increase in hospitalisations and XBB is reported to be more transmissible than previous sub-variants, it is also less severe.

Some reports describe XBB as a kind of "escape artist", but the Institute for Health Metrics and Evaluation said it "does not appear to have immune escape with BA.5 [an Omicron sub-variant], meaning individuals who were previously infected with BA.5 will maintain their immunity against the new sub-variant".

Dr Senanayake said Singapore had a very high vaccination rate of more than 90 per cent.

Dr Sheel said although XBB is spreading faster and indicates a level of immune evasion from the original Omicron variant, vaccines were key and there were lessons from looking at Singapore.

"What the experience of Singapore is showing is that, despite the vaccine coverage, despite the national immunity, we can still see an increase in cases and that new variants are coming and still causing these, I guess it could be a blip, or a wave of infection," she said.

"We need to be alert from a public health response perspective. We can't just stop, because we still have elderly and immunocompromised people at risk in the population.

"If your health workers start getting reinfected, then it becomes a challenge for your healthcare system."

Vaccinate before you travel
In South-East Asia, Indonesia has just wrapped up its hosting of the G20 in Bali.

One of the attendees – Cambodian Prime Minister Hun Sen – tested positive for COVID and left the country.

Cases in the world's fourth largest country are seeing a slight rise, but COVID measures recently re-introduced in Bali appeared to be more about the global summit than stopping the spread.

Epidemiologist Jane Soepardi said the XBB variant had arrived in Indonesia but was not dominant in the country yet.

Another consideration was the quality of surveillance, with cases under-reported globally.

"The tests in Indonesia are very low. It's very under diagnosed, under reported," Dr Soepardi said.

"High cases are always in Jakarta — this is very biased here, because in Jakarta there are so many tests and you can easily get tested for free, while in other provinces, it's not so."

Dr Soepardi said there should be more testing in tourist areas for peace of mind, adding that the isolation period in the country is 10 days.

She said government officials had to remind people of current restrictions.

"Now we have seen more cases, it's arising. So people are forgetting about this pandemic," she said.

Dr Senanayake said Indonesia had a lower vaccination coverage than some other countries.

But he said the development of their own vaccine – which has been declared halal for Muslims – might help.

"That's a good thing for Indonesia – their own homegrown vaccine, something they can be proud of, and less suspicious of, and that might help vaccine cases," he said.

Thailand too has recently developed its own vaccine – a homegrown mRNA shot.

Dr Senanayake said Thailand had good public health messaging during the pandemic and a robust health system.

"They've got pretty good public health infrastructure … the way they look after certain infections like dengue," he said.

For many countries in the region, travel and tourism are key to their economies.

"When you're not a rich country, it does come down to an important decision between tourism and health," he said.

"A lot of other countries, it's a matter of being able to feed your family by having the borders open versus not having COVID but dying from starvation. They're the realities."

Dr Sheel said we now have Omicron-specific vaccines available.

"I think the best thing people can do is make sure they're vaccinated before they travel," Dr Sheel said.

"The key is we know the vaccines work against more severe forms of disease, and the vaccine was always meant to protect people from dying, essentially."

Other steps include hand hygiene, isolating if you have a respiratory illness, wearing a mask in crowded places, and gathering outside over Christmas.

"It offers individual protection, community level protection to some extent Those are the key things that people can do at an individual level, that then contributes to population health."