HomeMy WebLinkAbout06.23.21 Variants Report_Redacted
From:York, Danette
To:Alpert, Bruce;Bennett, Robin;Clerk of the Board;Connelly, Bill;Cook, Holly;Cook, Robin;Hironimus, Patrizia;
Kimmelshue, Tod;Lucero, Debra;Paulsen, Shaina;Pickett, Andy;Reaster, Kayla;Ring, Brian;Ritter, Tami;
Sweeney, Kathleen;Teeter, Doug
Cc:Kim, Sang
Subject:Variants Report
Date:Wednesday, June 23, 2021 12:01:09 PM
Attachments:nCoV-2_VariantReport-20200611-FINAL.pdf
The Public Health Epidemiology/Data team has put together the attached variant report. The plan is
to update this report every two weeks and I will share it with you each time it comes out.
Yesterday, Supervisor Kimmelshue asked about the number of the Delta variant cases we have in
Butte County. You will see as of 6/11/2021 (date of this report) there were zero Delta variant cases. I
checked again this morning and as of today there are still zero cases of the Delta variant. I got
another variant confused with Delta yesterday when I answered the question. Again, to date zero
cases of the Delta variant, sorry for the confusion.
Respectfully,
Danette York, MPH, CPH
Public Health Director
BUTTE COUNTY PUBLIC HEALTH
202 Mira Loma Drive | Oroville, CA 95965
T: 530.552.4000 | D: 530.552.3820 | | M:
COVID-19 Call Center: 530.552.3050 Open 8:00 am - 4:30 pm, M-F
“Nationally Accredited, 09/13/17”
FACEBOOK | TWITTER
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and permanently delete the original and any copies of this e-mail and any attachments thereto.
From: Reyes, Elena <EReyes@buttecounty.net>
Sent: Tuesday, June 22, 2021 1:02 PM
To: Cox, Erin <ECox@buttecounty.net>; York, Danette <DYork@buttecounty.net>; Lewis, Linda
<llewis@buttecounty.net>; Bernstein, Robert <RBernstein@buttecounty.net>; Soderstrom, Monica
<msoderstrom@buttecounty.net>; Almaguer, Lisa <LAlmaguer@buttecounty.net>
Subject: Re: Variants report
Thank you!
Reports will be stored in:
CD\\CD_Secured\\COVID-19\\Epi Team\\Variants\\Biweekly Reports
Pdf attached
From: Cox, Erin <ECox@buttecounty.net>
Sent: Tuesday, June 22, 2021 12:59 PM
To: York, Danette <DYork@buttecounty.net>; Lewis, Linda <llewis@buttecounty.net>; Bernstein,
Robert <RBernstein@buttecounty.net>; Soderstrom, Monica <msoderstrom@buttecounty.net>;
Almaguer, Lisa <LAlmaguer@buttecounty.net>
Cc: Reyes, Elena <EReyes@buttecounty.net>
Subject: Re: Variants report
Great information. Thank you for creating and sharing. I will share this within the Covid
division as well for visibility with the team.
Erin
Erin Cox, MHS
Division Director, COVID
BUTTE COUNTY PUBLIC HEALTH
82 Table Mountain Blvd | Oroville, CA 95965
c
ECox@buttecounty.net
COVID-19 Call Center: 530.552.3050 Open 8 am- 4:30 pm M-F
“Nationally Accredited, 09/13/17”
FACEBOOK | TWITTER
COUNTY OF BUTTE E-MAIL DISCLAIMER: This e-mail and any attachment thereto may contain private,
confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or
distribution of this e-mail (or any attachments thereto) by other than the County of Butte or the intended
recipient is strictly prohibited. If you are NOT the intended recipient, please contact the sender immediately
and permanently delete the original and any copies of this e-mail and any attachments thereto.
From: York, Danette <DYork@buttecounty.net>
Sent: Tuesday, June 15, 2021 14:36
To: Lewis, Linda <llewis@buttecounty.net>; Bernstein, Robert <RBernstein@buttecounty.net>;
Soderstrom, Monica <msoderstrom@buttecounty.net>; Cox, Erin <ECox@buttecounty.net>;
Almaguer, Lisa <LAlmaguer@buttecounty.net>
Cc: Reyes, Elena <EReyes@buttecounty.net>
Subject: RE: Variants report
Great, thank you. I think Supervisor Lucero would really appreciate it but I also know she will share it
widely.
Respectfully,
Danette York, MPH, CPH
Public Health Director
BUTTE COUNTY PUBLIC HEALTH
202 Mira Loma Drive | Oroville, CA 95965
T: 530.552.4000 | D: 530.552.3820 | | M:
COVID-19 Call Center: 530.552.3050 Open 8:00 am - 4:30 pm, M-F
“Nationally Accredited, 09/13/17”
FACEBOOK | TWITTER
COUNTY OF BUTTE E-MAIL DISCLAIMER: This e-mail and any attachment thereto may contain private,
confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or
distribution of this e-mail (or any attachments thereto) by other than the County of Butte or the intended
recipient is strictly prohibited. If you are NOT the intended recipient, please contact the sender immediately
and permanently delete the original and any copies of this e-mail and any attachments thereto.
From: Lewis, Linda <llewis@buttecounty.net>
Sent: Tuesday, June 15, 2021 2:18 PM
To: York, Danette <DYork@buttecounty.net>; Bernstein, Robert <RBernstein@buttecounty.net>;
Soderstrom, Monica <msoderstrom@buttecounty.net>; Cox, Erin <ECox@buttecounty.net>;
Almaguer, Lisa <LAlmaguer@buttecounty.net>
Cc: Reyes, Elena <EReyes@buttecounty.net>
Subject: RE: Variants report
Hi Danette
That is up to you. I have no problem with this being shared.
Linda S Lewis, DVM, MPVM
Health Scientist, Community Health & Sciences
Butte County Public Health
llewis@buttecounty.net
P 530-552-3944 |F 530-538-5387
COUNTY OF BUTTE E-MAIL DISCLAIMER: This e-mail and any attachment thereto may contain private, confidential, and privileged material for
the sole use of the intended recipient. Any review, copying, or distribution of this e-mail (or any attachments thereto) by other than the County
of Butte or the intended recipient is strictly prohibited. If you are NOT the intended recipient, please contact the sender immediately and
permanently delete the original and any copies of this e-mail and any attachments thereto.
From: York, Danette <DYork@buttecounty.net>
Sent: Tuesday, June 15, 2021 2:14 PM
To: Lewis, Linda <llewis@buttecounty.net>; Bernstein, Robert <RBernstein@buttecounty.net>;
Soderstrom, Monica <msoderstrom@buttecounty.net>; Cox, Erin <ECox@buttecounty.net>;
Almaguer, Lisa <LAlmaguer@buttecounty.net>
Cc: Reyes, Elena <EReyes@buttecounty.net>
Subject: RE: Variants report
Just a couple of comments from me.
So, you do not want this shared outside the department?
Respectfully,
Danette York, MPH, CPH
Public Health Director
BUTTE COUNTY PUBLIC HEALTH
202 Mira Loma Drive | Oroville, CA 95965
T: 530.552.4000 | D: 530.552.3820 | | M:
COVID-19 Call Center: 530.552.3050 Open 8:00 am - 4:30 pm, M-F
“Nationally Accredited, 09/13/17”
FACEBOOK | TWITTER
COUNTY OF BUTTE E-MAIL DISCLAIMER: This e-mail and any attachment thereto may contain private,
confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or
distribution of this e-mail (or any attachments thereto) by other than the County of Butte or the intended
recipient is strictly prohibited. If you are NOT the intended recipient, please contact the sender immediately
and permanently delete the original and any copies of this e-mail and any attachments thereto.
From: Lewis, Linda <llewis@buttecounty.net>
Sent: Tuesday, June 15, 2021 1:51 PM
To: Bernstein, Robert <RBernstein@buttecounty.net>; York, Danette <DYork@buttecounty.net>;
Soderstrom, Monica <msoderstrom@buttecounty.net>; Cox, Erin <ECox@buttecounty.net>;
Almaguer, Lisa <LAlmaguer@buttecounty.net>
Cc: Reyes, Elena <EReyes@buttecounty.net>
Subject: Variants report
Good afternoon
Attached is a proposed bi-weekly variants report
Elena is lead on tracking whole genome sequencing data and creating this informational report.
(excellent work Elena!)
Our plan is to produce this report every 2 weeks for internal use and for use as background for BOS
meetings and PIO use.
The data and tables will be updated with each report. The explanatory section on Variants will be
updated as CDC makes changes to the designation of variants.
Please review and let us know if you have any suggestions. (If you catch any typos or errors, please
let me know – they are probably my doing)
Note that this report does NOT include our most recent cluster of 4 P1 (gamma) variants that came
in over this past weekend.
Linda S Lewis, DVM, MPVM
Health Scientist, Community Health & Sciences
Butte County Public Health
llewis@buttecounty.net
P 530-552-3944 |F 530-538-5387
COUNTY OF BUTTE E-MAIL DISCLAIMER: This e-mail and any attachment thereto may contain private, confidential, and privileged material for
the sole use of the intended recipient. Any review, copying, or distribution of this e-mail (or any attachments thereto) by other than the County
of Butte or the intended recipient is strictly prohibited. If you are NOT the intended recipient, please contact the sender immediately and
permanently delete the original and any copies of this e-mail and any attachments thereto.
Public Health Department Danette York, M.P.H., Director
Robert Bernstein, M.D., Health Officer
COVID Division - Oroville
202 Mira Loma Drive
buttecounty.net/publichealth
Oroville, California 95965
(Preliminary Data)
Progress of Butte County Variants
As of this report, Alpha (B.1.1.7), is the dominant variant in Butte County, comprising
88.9% of specimens sequenced in the month of May. Figure 1 and Table 1 show the
proportions of Variants of Concern (VOCs) and Variants of Interest (VOIs) among specimens
sequenced in Butte County, as defined by the CDC. Please see Page 3 Classifications of
SARS-CoV-2 Variants for these definitions.
The specimens tested represent a non-random sample of specimens from Butte County
residents. Specimens may be tested by commercial, academic, or state or federal public health
labs. Some specimens are collected as part of surveillance programs, some as routine
diagnostic testing or screening programs, and others are requested based upon severity of
illness, history of vaccination, or epidemiologic importance. As such, these data should be
interpreted cautiously as they may not be representative of all cases in Butte County.
Figure 1. Percent of Identified Variants of Concern (VOC) and Variants of interest (VOI) among all Specimens
Sequenced in Butte County as of June 4, 2021 by Month of Specimen Collection (N = 182)
Interest (VOI) or Concern (VOC) or High
Consequence (VOHC)
6/11/2021 1
Table 1. Percent of identified Variants of Concern(VOC) and Variants of interest (VOI) out of all Specimens
Sequenced in Butte County as of June 4, 2021 by Month of Specimen Collection (N = 182)
Specimen
Collection Alpha Beta Gamma Epsilon Epsilon Zeta Eta Iota Kappa
Month(B.1.1.7)(B.1.351)(P.1)(B.1.429)(B.1.427)(P.2)(B.1.525)(B.1.526)(B.1.617)*
May-2188.9%0.0%0.0%0.0%0.0%0.0%0.0%5.6%0.0%
Apr-2185.2%0.0%1.6%9.8%0.0%0.0%0.0%0.0%0.0%
Mar-2133.3%0.0%0.0%40.0%0.0%0.0%0.0%0.0%0.0%
Feb-212.9%0.0%0.0%37.1%14.3%0.0%0.0%0.0%0.0%
Jan-210.0%0.0%0.0%12.5%0.0%0.0%0.0%0.0%0.0%
Dec-200.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%
Nov-200.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%
Oct-200.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%
Sep-200.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%
Aug-200.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%
Jul-200.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%0.0%
Statewide data by CDPH variant can be found at https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/COVID-
19/COVID-Variants.aspx. Totals shown for Kappa (B.1.617) will also include sub lineages B.1.617, B.1.617.2,
and B.1.217.3.
Refer to Figure 2 and Figure 3 below in order to compare Butte County with variant progress
statewide.
Figure 2 Percent of identified Variants of Concern (VOC) and Variants of interest (VOI) out of all Specimens
Sequenced in California as of June 9, 2021 by Month of Specimen Collection
6/11/2021 2
Figure 3. Percent of identified Variants of Concern(VOC) and Variants of interest (VOI) out of all Specimens
Sequenced in California as of June 9, 2021 by Month of Specimen Collection
1
Classifications of SARS-CoV-2 Variants
Variants of High Consequence (VOHC)
Compared with previously circulating variants, clear evidence of:
- a significant reduction in the effectiveness of prevention measures, including vaccination
- demonstrated failure of diagnostics
- a significant reduction in the effectiveness of treatment
Currently, there are no variants that rise to the level of a VOHC in the US or globally.
Variants of Concern (VOC):
A variant for which there is evidence of:
An increase in transmissibility
An increase in disease severity (e.g., increased hospitalizations or deaths), or
1
Based on CDC classifications, found here: https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-
info.html?CDC_AA_refVal=https%3A%2F%2Fwww.cdc.gov%2Fcoronavirus%2F2019-ncov%2Fcases-
updates%2Fvariant-surveillance%2Fvariant-info.html
6/11/2021 3
A significant reduction in neutralization by antibodies (i.e. effectiveness of antibodies)
generated during previous infection or vaccination, reduced effectiveness of treatments
or vaccines, or failures of diagnostic tests to detect the variant.
As of June 14, five CDC-designated variants of concern have been identified in
California, and four identified in Butte County:
Table 2. Known Variants of Concern in California and Butte County, as of June 4th, 2021
Cases Caused by Cases Caused by
VariantWHO LabelVariant, CAVariant, Butte
B.1.1.7Alpha8,88274
B.1.351Beta1020
P.1Gamma1,2101
B.1.427Epsilon6,8125
B.1.429Epsilon12,94126
Table above based on CDPH variant tracking found here.
Variants of Interest (VOI):
A variant with specific genetic markers that are predicted to increase transmission, decrease the
effectiveness of diagnostics or treatments, or decrease immunity acquired through prior
infection or vaccination.
Five CDC-designated variants of interest have been identified in California, and one
identified in Butte County:
Table 3. Known Variants of Interest in California and Butte County, as of June 4th, 2021
Cases Caused by Cases Caused by
VariantWHO LabelVariant, CAVariant, Butte
B.1.5261
0
available
0
0
0
Table above based on CDPH variant tracking found here. Totals shown for Kappa (B.1.617) also include sub
lineages B.1.617, B.1.617.2, and B.1.217.3
6/11/2021 4