BA.2.12.1 is on the rise in New York…

A recently named sub-strain represents the latest twist in the ongoing evolution of SARS-CoV-2. It’s currently active in the United States and looks to be very capable of spreading, outpacing the base model BA.2. As usual, it’s early days so we don’t know a lot about BA.2.12.1 and disease severity or how much protection is offered by previous vaccination. It seems BA.2.12.1 is likely to visit a host near you in 2022.

Analysis of some genomes shows the rise of BA.2.12.1

The US CDC genomic sequencing data page shows this variant’s rise to the week ending 23rd of April. They also model its likely ongoing rapid spread.[2,5]

Graph from the US Centers for Disease Control and Prevention (CDC) COVID data tracker, variant proportions website.[2]

BA.2.12.1 has also been highlighted on NEXTSTRAIN – a gold standard resource for following the emergence and changes of a range of important viruses.[2]

Dr Emma Hodcroft notes NEXTSTRAIN has made a place for some new clades in the forest of SARS-CoV-2, and this includes BA.2.12.1 (22C).[3] See the NEXTSTRAIN blog on this image.[4]

Remember that sequencing is a lagging indicator – what we see now, happened in the past. The lag can be bigger or smaller depending on the source.

Genomic sequencing usually shows only the tip of the iceberg. It shouldn’t be used to define the number of cases in an area unless every case is a) captured (some sites are better than others) and b) can be sequenced (depends on sampling, sample handling, whereabouts in the course of the disease the person is, CT, sequencing method, data analysis, etcetera).

Drawing conclusions about changes in virus proportions based on viral genome sequencing is subject to from whom, where and when samples were collected; do they represent what we assume when we look at the data? What proportion cam from hospitalised patients, cases of special interest, asymptomatic cases, are they from a fixed percentage of cases, are they from all over the land, is there a proportional representation of locals and travellers…and so on.

Hospitalised cases are on the rise in New York

Given this apparent rise in BA.2.12.1 viruses in New York COVID-19 cases, it’s also very interesting to look at hospitalisations. Here we find that there’s been a rise in hospitalised cases as well.[1]

Graph from New York State Health Department’s novel coronavirus hospitalisation summary.[1]

BA.2.12.1 is already travelling

With an estimated transmission advantage of 23% – 27% over the original BA.2,[14] it’s no surprise BA.2.12.1 is on the move. Other States in the US have already reported cases,[13] and it’s been detected in a case in Delhi, India [17], among two local cases in Singapore [16] and in the wastewater of the Australian State of Victoria.[15,6]

We know what we can do

There are a few things we know can help us avoid getting sick from circulating respiratory viruses like SARS-CoV-2.

Getting boosted is top of the list

Our immunity to anything drops off over time.

We’ve learned in the pandemic that the first to go is the relatively short-lived immunity that protects from infection (virus getting a foothold in our airways).

The next to go is immunity against more severe disease but that isn’t necessarily because the vaccine-generate immunity has disappeared, but more because SARS-CoV2 keeps evolving. That other slippery virus we know so well, the influenza virus, does a similar thing. So we have to change the flu vaccine annually to keep up with the rapidly evolving flu viruses.

When viruses like SARS-CoV-2 and influenza virus spread through so many humans, each infection giving rise to a swarm of mutants, there are more chances (because more hosts) that a “fitter” virus will emerge. In this context, fitness relates to a virus changed enough to be able to doge some of our immune response. We’ll learn more about what BA.2.12.1 can do as time goes by.

Air purity

While not accessible to everyone,[18-19] even in richer nations, we expect our food to be fresh and clean and we expect our water to be toxin and pathogen-free. These two things, when present and working, save lives and prevent a lot of diseases.

The next big revolution in public health is to purify pathogens out of the air we share.[9-12]

If we did this, we would dramatically reduce acute and chronic diseases, reduce sick days and lost education days and hospital and aged care disease outbreaks.

Masks

They don’t hurt and, if you use good ones (e.g. P2/N95) and they fit well and you wear them whenever there is a risk, you’ll reduce the likelihood of inhaling enough virus to get sick.

References

  1. Novel coronavirus, Daily Hospitalisation Summary
    https://coronavirus.health.ny.gov/daily-hospitalization-summary
  2. COVID Data Tracker – Variant Proportions
    https://covid.cdc.gov/covid-data-tracker/#variant-proportions
  3. Genomic epidemiology of SARS-CoV-2 with subsampling focused globally over the past 6 months
    https://nextstrain.org/ncov/gisaid/global/6m
  4. SARS-CoV-2 clade naming strategy for 2022 9last visited, 02MAY2022 AEST)
    https://nextstrain.org/blog/2022-04-29-SARS-CoV-2-clade-naming-2022
  5. New Omicron Variant BA.2.12.1 Now Dominant In New York, Driving Infections; Strain Up 47% Nationwide In Past Week
    https://deadline.com/2022/04/new-omicron-variant-ba-12-1-dominant-new-york-1235010160/
  6. COVID-19 Omicron subvariant BA.2.12.1 detected in Australia in Victorian wastewater
    https://www.abc.net.au/news/2022-04-30/covid-19-omicron-subvariant-ba-2-12-1-detected-in-victoria/101027818
  7. Survival Of The Fittest: The Rise Of BA.2.12.1
    https://www.forbes.com/sites/williamhaseltine/2022/04/22/survival-of-the-fittest-the-rise-of-ba2121/?sh=29687b5b413d
  8. Portable air cleaners and residential exposure to SARS-CoV-2 aerosols: A real-world study
    https://pubmed.ncbi.nlm.nih.gov/35481935/
  9. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals
    https://www.nature.com/articles/s41586-020-2271-3
  10. Use of portable air purifiers as local exhaust ventilation during COVID-19
    https://pubmed.ncbi.nlm.nih.gov/35290164/
  11. Airborne SARS-CoV-2 in hospitals – effects of aerosol-generating procedures, HEPA-filtration units, patient viral load and physical distance
    https://pubmed.ncbi.nlm.nih.gov/35226740/
  12. Use of portable air cleaners to reduce aerosol transmission on a hospital coronavirus disease 2019 (COVID-19) ward
    https://www.cambridge.org/core/journals/infection-control-and-hospital-epidemiology/article/abs/use-of-portable-air-cleaners-to-reduce-aerosol-transmission-on-a-hospital-coronavirus-disease-2019-covid19-ward/17C5199D3903ABD465017C34AA741826
  13. A new omicron subvariant is spreading in North Texas: What we know about BA.2.12.1
    https://www.star-telegram.com/news/coronavirus/article260860897.html
  14. New York State Department of Health Announces Emergence of Recently Identified, Highly Contagious Omicron Subvariants in New York and Urges Continued Vigilance Against COVID-19
    https://www.health.ny.gov/press/releases/2022/2022-04-13_covid-19.htm
  15. Coronavirus update for Victoria – 29 April 2022
    https://www.health.vic.gov.au/media-releases/coronavirus-update-for-victoria-29-april-2022
  16. 2 S’pore Covid-19 cases infected with new Omicron sub-variant BA.2.12.1
    https://www.straitstimes.com/singapore/health/two-singapore-covid-19-cases-infected-with-new-sub-variant-of-omicron-ba2
  17. Omicron’s BA.2.12.1 mutant found in a Delhi patient, all you need to know about the sub-variant
    https://www.dnaindia.com/india/report-omicron-ba-2-12-1-mutant-found-in-a-delhi-patient-all-you-need-to-know-about-the-sub-variant-2947595
  18. Calls for clean water continue
    https://nit.com.au/calls-for-clean-water-continue/
  19. Uranium Detectable in Two-Thirds of U.S. Community Water System Monitoring Records
    https://www.publichealth.columbia.edu/public-health-now/news/uranium-detectable-two-thirds-us-community-water-system-monitoring-records

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