Local (and not-so-local) COVID-19 updates

[edschweppe]

Unsurprisingly, the state took yesterday off:

Please note: The daily COVID-19 Interactive Data Dashboard was not posted on Thanksgiving Day, Thursday, November 25. Data from Wednesday, November 24 to Thursday, November 25 is included in the dashboard posted on Friday, November 26.

So what do we get for two days of data?

As of 5PM today, the Commonwealth of Massachusetts is reporting 24 newly reported confirmed deaths (6 more than Wednesday - up 33.3%) for a total of 18,939 deaths, 5,058 newly reported confirmed cases (2,080 more than Wednesday - up 69.8%) for a total of 847,030 cases, and 171,111 newly reported molecular tests (58,328 more than Wednesday - up 51.7%).

Note that today's data covers 2 days. Averaged over that period, there were 12.0 newly reported deaths per day (6 less than Wednesday - down 33.3%), 2,529.0 newly reported cases per day (449 less than Wednesday - down 15.1%), and 85,555.5 newly reported molecular tests per day (27,228 less than Wednesday - down 24.1%).

The seven day average positivity rate is 3.37%, compared to 3.31% Wednesday. The state also reported zero newly reported probable deaths (2 less than Wednesday) for a total of 412 and 240 newly reported probable cases (204 less than Wednesday - down 45.9%) for a total of 62,675. Combining the confirmed and probable numbers gives 24 new deaths for a total of 19,351 and 5,298 new cases for a total of 909,705. There were 771 COVID-19 patients in hospital (7 more than Wednesday - up 0.9%), 156 COVID-19 patients in ICUs (9 less than Wednesday - down 5.5%) and 84 COVID-19 patients on ventilators (intubated) (5 less than Wednesday - down 5.6%).

Of the four overview trends (formerly the Page 2 "key metrics"), the 7-day average of newly confirmed cases is 1,940.0 (58 less than Wednesday - down 2.9%), 2,931% above the lowest observed value of 64.0 on 6/25/2021 and 69.0% below the highest observed value of 6,229.0 on 1/8/2021. The 7-day weighted average of positive molecular test rate is 3.37% (0 more than Wednesday - up 1.7%), 993% above the lowest observed value of 0.3% on 6/25/2021 and 88% below the highest observed value of 27.7% on 4/15/2020. The 7-day average number of COVID-19 patients in hospital is 718.0 (27 more than Wednesday - up 3.9%), 744% above the lowest observed value of 85.0 on 7/9/2021 and 82% below the highest observed value of 3,874.0 on 4/27/2020. The 7-day average number of COVID-19 deaths is 12.0 (1 more than Wednesday - up 9.1%), 1,100% above the lowest observed value of 1.0 on 7/11/2021 and 94% below the highest observed value of 175.0 on 4/24/2020.

Statewide, hospitals reported 8,927 non-ICU beds, of which 7,024 (78.7%) were occupied by non-COVID patients, 615 (6.9%) were occupied by COVID patients, and 1,288 (14.4%) remained available. Hospitals also reported 1,245 ICU beds, of which 842 (67.6%) were occupied by non-COVID patients, 156 (12.5%) were occupied by COVID patients, and 247 (19.8%) remained available. By comparison, hospitals reported Wednesday a total of 8,987 non-ICU beds, of which 7,549 (84.0%) were occupied by non-COVID patients, 599 (7%) were occupied by COVID patients, and 839 (9.3%) remained available. Hospitals also reported Wednesday a total of 1,259 ICU beds, of which 889 (70.6%) were occupied by non-COVID patients, 165 (13.1%) were occupied by COVID patients, and 205 (16.3%) remained available.

Two weeks ago, the 7 day confirmed case average was 1,233.0, the 7 day confirmed deaths average was 9.0, the 7 day hospitalization average was 518.0, and the 7 day weighted average positivity rate was 2.32% (or 4.11% excluding higher education).

Today being Friday (and yesterday having been a holiday), the state also included city/town specific information in the daily download. My town of Acton is listed as having 1,257 total cases, with a two-week case count of 74 cases, a daily incidence rate of 22.3 which is higher than last week, with a corresponding risk color code of yellow (if the state was still reporting color codes). Acton is also listed as having 72,005 total tests, with a two-week total test count of 2,460 and a two-week positive test count of 76, for a percent-positive rate of 3.09 which is higher than last week. The corresponding statewide figures are 841,972 total cases, with a two-week case count of 29,741 cases, a daily incidence rate of 30.5 which is higher than last week. Massachusetts is also listed as having 33,104,252 total tests, with a two-week total test count of 1,129,264 and a two-week positive test count of 32,679, for a percent-positive rate of 2.89 which is higher than last week.

As of July 1, 2021, the state is no longer reporting risk color codes. However, if it was, of the 351 cites and towns in the Commonwealth, 75 would be coded gray (compared to 97 last week), 23 would be coded green (compared to 23 last week), and 131 would be coded yellow (compared to 166 last week).The remaining 122 towns would be coded red (compared to 65 last week): Abington, Acushnet, Adams, Agawam, Amesbury, Ashburnham, Athol, Attleboro, Ayer, Barnstable, Bellingham, Berkley, Beverly, Billerica, Blackstone, Bourne, Boxford, Brewster, Bridgewater, Charlton, Chelmsford, Cheshire, Chicopee, Clinton, Dalton, Danvers, Dartmouth, Dennis, Dighton, Douglas, Dracut, Duxbury, East Bridgewater, East Brookfield, Essex, Fairhaven, Fall River, Fitchburg, Freetown, Gardner, Georgetown, Gloucester, Great Barrington, Groveland, Halifax, Hamilton, Hanson, Harwich, Haverhill, Holland, Hubbardston, Kingston, Lakeville, Lancaster, Lanesborough, Lawrence, Littleton, Lowell, Lunenburg, Lynn, Lynnfield, Marshfield, Mattapoisett, Medfield, Merrimac, Methuen, Middleborough, Middleton, New Bedford, Newbury, North Attleborough, Northbridge, Orange, Orleans, Paxton, Peabody, Pembroke, Pepperell, Pittsfield, Plainville, Plymouth, Rehoboth, Revere, Rochester, Rockport, Rowley, Rutland, Salem, Salisbury, Sandwich, Saugus, Scituate, Seekonk, Shirley, Southampton, Southborough, Southwick, Spencer, Springfield, Sterling, Sturbridge, Sutton, Swansea, Taunton, Templeton, Townsend, Tyngsborough, Upton, Uxbridge, Wakefield, Ware, Wareham, Wenham, West Boylston, West Bridgewater, West Brookfield, Westfield, Westford, Westminster, Whitman, Winchendon, and Yarmouth.

61 cities/towns would be newly coded red this week (Abington, Agawam, Attleboro, Barnstable, Berkley, Beverly, Bourne, Boxford, Brewster, Bridgewater, Chelmsford, Danvers, Dartmouth, Dighton, Duxbury, East Brookfield, Essex, Fitchburg, Gloucester, Great Barrington, Groveland, Halifax, Hamilton, Hanson, Holland, Kingston, Lancaster, Lanesborough, Lunenburg, Marshfield, Medfield, Merrimac, Middleborough, Newbury, North Attleborough, Northbridge, Orleans, Pembroke, Pittsfield, Plainville, Revere, Rockport, Rowley, Rutland, Salem, Sandwich, Saugus, Scituate, Shirley, Southampton, Spencer, Springfield, Swansea, Wakefield, Ware, Wareham, Wenham, Westfield, Westford, Whitman, and Yarmouth) and 4 cities/towns would no longer be coded red this week (Nantucket, Newburyport, Stow, and Westport).

Of the 10 towns nearby (including my own town), one is coded gray (Carlisle), 2 are coded green (Boxborough, and Stow), 4 are coded yellow (Acton, Concord, Maynard, and Sudbury), and 3 are coded red (Chelmsford, Littleton, and Westford).

Of the 10 towns near my church, none are coded gray, 4 are coded green (Berlin, Bolton, Boxborough, and Stow), 6 are coded yellow (Acton, Harvard, Hudson, Marlborough, Maynard, and Sudbury), and none are coded red.

The daily raw data file used to create this report is available here.

Well, we get a borked data file, for starters, which required a bit of hacking around. Then we get what might look at first like decent news, as newly reported deaths and cases are both down compared to Wednesday's report, if you average today's numbers over two days. On the other hand, only 49 of those newly reported cases were from tests that were dated yesterday, which shouldn't surprise me too much since yesterday was a holiday; I suspect that count would have been much, much higher if not for the holiday. Besides, twenty-five-hundred cases a day isn't good news under any circumstances. Hospitalizations are up as is percent-positive. The city and town data that normally shows up on Thursdays was reported today, and that's pretty bad news as well. If the state were still reporting risk codes, the number of communities at highest risk would have almost doubled to 122, including three near my town of Acton (which isn't red yet, but is continuing to see a rapid rise in cases; see the end of this post).

And, just in case that wasn't enough bad news for a Friday, there's a new and potentially extra-nasty coronavirus variant (B.1.1.529) out there, with the World Health Organization designating it "omicron":

Scientists in South Africa have identified a new coronavirus variant with a worrisome combination of mutations that experts fear could make it more transmissible and allow it to evade immune protection — including the protection generated by vaccines.

Experts are scrambling to learn more about the variant, known by its scientific name B.1.1.529 and called Omicron by the World Health Organization. Right now, there are more open questions than firm answers. And although scientists have expressed significant early concern over the variant — the WHO designated it as a "variant of concern" on Friday — they have cautioned that they are still seeking critical information about it.

Below, STAT outlines what is known and unknown.

One reminder: There have been a series of variants that have caused initial alarm, only to prove largely unimportant in the course of the pandemic.

Where has it been detected?

Scientists in South Africa detected the lineage on Monday, according to the country's National Institute for Communicable Diseases, and rang the alarm bell for the world. Researchers in Botswana and Hong Kong also posted sequences publicly, and other cases have since been reported in Belgium and Israel. The variant is likely in other countries, but researchers just haven't picked it up yet.

It's not clear where the variant actually emerged. It could be that South Africa and Botswana saw it early because they have strong genetic sequencing networks.

On Friday afternoon, the United States joined other countries in imposing travel restrictions from those two countries, as well as Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique, and Malawi, effective Monday.

Why is it causing concern?

Several reasons.

For one, it appears to be outcompeting other variants in South Africa — including the extremely transmissible Delta variant — and fast. It's starting to drive cases up in that country, which has already had several massive waves in its epidemic. Some possible explanations are that it's a better spreader than even Delta, that it can cause infections in people who are protected at higher rates, or some combination of the two.

But beyond the epidemiological landscape in South Africa, scientists are concerned because of the number and variety of mutations B.1.1.529 acquired — what Sharon Peacock, the director of the Covid-19 Genomics UK Consortium, called a "very unusual constellation of mutations." Some mutations have been previously seen in other variants and are associated with increased transmissibility and the ability to get around immune protection.

Scientists can't predict how different mutations will behave when combined, but of particular worry to scientists is that the virus has some 32 mutations in its spike protein, which is what vaccines teach our immune system to recognize and target.

The variant "has a very high number of mutations with a concern for predictive immune evasion and transmissibility," said Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation, who helped identify the variant in South Africa.

What does it mean for immune protection?

If the spike protein changes, the antibodies elicited by vaccines or an earlier infection can't recognize it as well. The more changes, the more foreign that spike starts to look to the immune system.

Vaccines generate what's called a polyclonal response, with lots of antibodies that recognize different pieces of the spike protein. Other variants have had mutations that caused changes in a particular spot on the protein — called an antigenic site — and might have thrown off those corresponding antibodies, but there were plenty of other antibodies that still could recognize the virus.

But with the new variant, "it has so many changes across spike that nearly all the antigenic sites we know about are changed on this virus," said Wendy Barclay, who leads a U.K. group studying new variants of the SARS-CoV-2 coronavirus. That suggests, Barclay said, that the ability of antibodies "will be compromised in their ability to neutralize the virus" — though she cautioned that scientists need to study that question to confirm it.

So far, researchers don't know exactly what size dent the variant might have on vaccine effectiveness; the question of immune escape is one of degrees, not all or nothing. Some variants that have emerged so far have had more of an impact on vaccine effectiveness than others, though the vaccines so far have been able to keep up with the variants. Scientists have also found that it would take lots of escape mutations in the right spots to enable the virus to fully evade immunity.

[ ... ]

What does it mean for the rest of the world?

It's too early to say. Some variants have taken off globally — take Delta — but other variants that caused concerns, such as Beta and Gamma, never really established toeholds beyond the regions where they first emerged. Variants can behave differently in different places, depending on what other versions of the virus are circulating and also on the levels of protection in a given place.

Well, shit. I doubt those travel bans will do much good, if it's already showing up in Europe and Asia.

Happy goddamn weekend, folks.

The town of Acton's current Google Data Studio dashboard is showing 64 active and 1,329 cumulative cases as of November 25; the 64 active cases are the most the town has reported since it reported 66 cases on January 19. The most recent "newsflash style update" at 1PM on November 22, 2021 reported 1304 cumulative cases with 54 individuals in isolation, 1218 persons recovered and 32 fatalities.