A post on the AY.4 sub-lineage of the Delta Sars-Cov-2 variant. Also known as B.1.617.2.4, this sub-lineage hasn’t received a lot of press attention yet, but it seems to have become the biggest sub-lineage of Delta across the globe so far.
In the USA, the Delta AY.4 sub-lineage is currently appearing in about 20% of sequences (light blue area) according to Outbreak.info:
In the UK, AY.4 currently appears in about 46% of samples (light blue area), and is now outcompeting B.1.617.2 (dark blue area).
AY.6 seems to be coming up on the rails though at 3%:
In Australia, AY.4 (dark blue area) clearly predominates over B.1.617.2 (light blue area) with 67% of sequences, B.1.617.2 is at 16% and AY.12 is at 10% :
In the USA, the estimated number of AY.4 cases was over 80,000 in early August 2021:
In the UK, the estimated number of AY.4 cases was about 13,000 in late August 2021
In Australia, the estimated number of cases was over 600 in late August 2021
In the USA, the demographics for AY.4 show it spreading across almost all age ranges,
But in the UK, AY.4 seems to be spreading amongst young children:
And in Australia, AY.4 seems to be spread across all age ranges:
The global reach of the AY.4 sub-lineage is really quite astounding considering it’s relatively recent appearance:
Further reading: New AY lineages and an update to AY.4-AY.12
“Sydney is on fire with this virus and we need a ring of steel around Sydney.”
Victorian Premier Daniel Andrews has called for more to be done after New South Wales Chief health officer Kerry Chant described the situation in NSW as ‘a national emergency’.
New South Wales recorded 136 local COVID-19 cases today, 53 of which were infectious in the community. Mr Andrews said New South Wales seemed to have “crossed a threshold” with a surge in COVID-19 cases.
The Trans-Tasman bubble that allows for travel between Australia and New Zealand has been closed “for at least 8 weeks according to RNZ.co.nz
Stunning headlines from the Sydney Morning Post today: “Do not leave your home’: Sydney bracing for weeks of lockdown”. Sydney is bracing for a lockdown that could stretch for weeks, with surging case numbers prompting tighter restrictions as the number of people in strict isolation doubled to 14,000 in a single day.
We are sending out this special update to alert you to the new (tighter) set of restrictions that will apply to Greater Sydney from 5pm today 9th July 2021. The existing four reasons to leave home remain unchanged. The restrictions in regional NSW also remain unchanged. From 5pm we must all remain within our own local government area, or within 10 kilometres of home for exercise and outdoor recreation.
- Outdoor public gatherings will be limited to two people
- No carpooling between non-household members
- Only one person per household, per day, may leave the home for shopping
- Browsing in shops is not allowed, only shopping for essentials
From Sunday, funerals will be limited to 10 people in total.
Overnight, 44 new cases were recorded of which 27 were out in the community for at least part of their infectious period.
The latest figures from NSW Health show there are 43 people with COVID-19 in hospital, 10 of whom are in intensive care. Four of the patients in ICU require ventilation.
Premier Gladys Berejiklian has also foreshadowed extending the lockdown beyond July 16.
NSW is facing “the biggest challenge we have faced since the pandemic started … unless there is a dramatic turnaround in the numbers, I can’t see how we would be in a position to ease restrictions by next Friday,” Ms Berejiklian said.
The most recent figures available to us show that 8.17 per cent of the population is fully vaccinated while 25.72 per cent have had one shot.
As Sydney’s lockdown entered its third week, there were signs of the outbreak spiralling, with a record increase of 38 new cases in the last 24 hours. The outbreak has nearly reached 400 cases, and is spreading quickly across the largely unvaccinated city.
Australia’s Prime Minister Scott Morrison has announced 300,000 coronavirus vaccine doses will be rushed to Sydney today, as the country’s largest city struggled to bring a Delta outbreak under control. Scott Morrison said the situation in the city was “very serious” and urged five million Sydney residents not to give in to fatigue and obey stay-at-home orders.
The Wellington region of New Zealand has been in coronavirus alert level 2 since last week after a man from Sydney travelled round the capital while he had the Delta variant of the virus.
The partner of the Sydney man infected with Covid-19 has tested positive. The couple visited several locations in Wellington before testing positive. The partner originally returned a negative test, but later tested positive. The trans-Tasman bubble has been closed due to the increasing number of cases coming to New Zealand from Australia.
Australian scientists have described how they used high-performance computer modelling of the form of the SARS-CoV-2 virus at the beginning of the pandemic to predict its ability to infect humans and a range of 12 domestic and exotic animals.
Surprisingly, the results showed that SARS-CoV-2 bound to ACE2 on human cells more tightly than any of the tested animal species, including bats and pangolins. If one of the animal species tested was the origin, it would normally be expected to show the highest binding to the virus.
“We also deduced that some domesticated animals like cats, dogs and cows are likely to be susceptible to SARS-CoV-2 infection too.”
Study: In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin
Greater Sydney, the Blue Mountains, the Central Coast and Wollongong will go into a 14-day lockdown as health authorities try to regain control of a coronavirus outbreak that has ballooned to 80 cases. Some 29 covid-19 cases were recorded in the 24 hours to 8pm on Friday, 17 of which had already been announced, taking the cluster to 80 cases.
The latest wave of Covid-19 in Australia seems to be driven largely by the recent introduction of the Delta variant B.1.617.2, following a pattern now seen worldwide.
From 6pm on Saturday, residents in the affected areas will only be able to leave home for essential reasons. People may only leave their homes for work, to shop for essential items, to seek medical care, or for care-giving or compassionate reasons.
Exercise outdoors is allowed in groups of up to 10, and Covid-safe funerals can proceed with up to 100 people. Weddings are allowed to go ahead on Saturday and Sunday with restrictions in place, but must be cancelled from Monday onwards. No more than five visitors are allowed for a household each day, masks are required indoors and restrictions apply to weddings and funerals.
The New South Wales premier says there has been one new covid case, that has come about as a result of “fleeting contact” in a shopping centre, and there are new restrictions for the state.
The one new locally acquired case since 8pm last night is a man in his 50s who had been to the Bondi Junction Westfield and came into contact with the infected limousine driver.
CCTV footage of the Bondi Junction’s Myer store puts the latest positive case on the same floor as the initial case on Saturday, but at this stage, Dr Kerry Chant says, authorities haven’t seen the moment of “fleeting contact” between the two.
“At the moment they have placed him in the same floor in the same section of Myer. They have asked for further CCTV footage to see if there is inadvertent passing,” she said.
“At the moment we don’t know the nature of the contact, the fact that the community would understand that, in general, when we are shopping in settings such as those sorts of retail environments we don’t generally come in close proximity.
“We just need to wait for the CCTV footage. You can’t recall everything that happens. There might be a close exposure.”
Australian health authorities are contacting scores of people in Western Australia after a man tested positive to COVID-19 after being released from the state’s quarantine hotels. Western Australia Chief Health Officer Dr Andrew Robertson said “We often get people who are chronic shedders, but the test result was more moderately positive than we would anticipate. So, as a precaution, we have put him back into one of the quarantine hotels and have taken further tests.”
The latest Melbourne outbreak is believed to have begun when a traveller infected with the Kappa variant (B16171) returned to Australia.
“We’ve got to run this thing to ground otherwise people will die,” Victoria’s acting state Premier James Merlino said, adding they were dealing with a virus variant “quicker and more contagious than we have ever seen before”.
Thousands of close contacts have been identified and the list of venues visited by the 60 confirmed cases has grown to about 350.
Australian COVID-19 testing commander Jeroen Weimar said authorities were now concerned about examples of transmission with very little contact between cases. “They’re brushing past each other in a small shop, they’re going around a display home … they’re looking at phones in a Telstra shop,” he said. “They don’t know each other’s names, and that’s very different from where we’ve been before. “We think it’s primarily a feature of the [Delta] variant which is that it is just that much more contagious.”
The risk of thrombosis at 11 excess events per 100 000 vaccinations are higher than estimated by the European Medicines Agency. The EMA estimates the risk of thrombosis to be between 1 and 2 per 100 000 people, depending on age. Among the venous thromboembolic events, the most notable was cerebral venous thrombosis, which was about 20 times more common after the Oxford-AstraZeneca vaccine than expected with an excess risk of 2.5 per 100 000 vaccinations. Venous thromboembolic events were more common in women than in men and were also more common in people aged 18-44 than in those aged 45-65. Thrombocytopenia and bleeding were mildly increased after vaccination, but not significantly.
Study Paper here: Arterial events, venous thromboembolism, thrombocytopenia, and bleeding after vaccination with Oxford-AstraZeneca ChAdOx1-S in Denmark and Norway: population based cohort study
Victoria, Australia has closed its border to Perth residents after a passenger infected with coronavirus landed at Melbourne Airport. The man caught the virus at a quarantine hotel in Perth after being in China and then flew to Melbourne without knowing he was a carrier.
On Friday night the case plunged Perth into a three-day lockdown after it was revealed the man had moved around the city for four days. The man who arrived is Victoria’s first community case of COVID-19 in eight weeks. All 257 passengers aboard the April 21 flight QF778 have been ordered to get tested and to isolate for 14 days.