Covid-19 tracker: the numbers are rising, the masks are falling

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Hello, Mission, and welcome to Virus Village, your (somewhat regular) Covid-19 data dump.

The number of infections, hospitalizations and positivity rates have increased slightly over the past week, while R Number models today show a slight decrease in the rate of transmission.

Yesterday the UCSF Grand Rounds featured a discussion of how the virus has evolved and what we can expect from rapid testing. The Biden administration yesterday announced new funding for more rapid home tests. I wish they had tackled the unusual pattern of the virus in San Francisco that has persisted for three weeks.

Despite the numbers, the big news today is that San Francisco is easing its interior masking requirements next week. While it can be difficult to figure out which places won’t require a mask, that’s how the Mayor explains it. For the foreseeable future, masks will still be required in restaurants and bars (where I have observed that very few people follow the rules for masking between bites and sips).

It can also be difficult to understand why the City is changing its policy. Criteria for relaxing the mask requirements are: 1) moderate transmission as determined by the CDC, 2) 80 percent of the total population fully vaccinated, and 3) low and stable hospitalizations. According to the latest data, SF is missing the first two and the third is a judgment call.

Others offer different ideas (metrics) to get out of the public health emergency.

Is the immunity offered by natural infection the same as the immunity given to you by The Vaccine? Although the infection is believed to confer some immunity, no one is sure exactly what immunity or how long it will last. Since no company takes advantage of natural immunity, few studies have been done on the subject, but here is one recently published, concluding “[t]The protective effect of a previous SARS-CoV-2 infection on re-infection is high and similar to the protective effect of vaccination, ”but that more research on the duration of protection and protection against variants are necessary.

New study in Italy shows that seven months after the second dose, there is no reduction in the effectiveness of COVID-19 mRNA vaccines in the general population, while a slight decrease is observed for some specific groups . However, recent data suggests an mRNA booster for those who have received the Johnson & Johnson vaccine. According to UCSF doc Monica Gandhi, UCSF is already providing a reminder “to anyone who has received Johnson & Johnson vaccines.”

Good news from the Dubs side: Andrew Wiggins got vaccinated. Kareem Abdul Jabbar has broadened his criticism of NBA stars who continue to refuse vaccination by calling out those like LeBron James and Draymond Green who defend them.

Here are other reasons why virology labs that handle viruses should stop. Now.

And for those who believe that genetics, rather than racial and income inequalities, cause health inequalities, it’s time to think again.

Scroll down for today’s covid numbers.

The U.S. Centers for Disease Control data used for the chart lags behind data provided by the San Francisco Department of Public Health. As of October 7, DPH was reporting more than 80 percent of all San Francisco residents received a dose, and 75 percent are fully vaccinated. The new vaccinations, although weak, continue to advance. On October 7, the moving average of seven days of shooting per day was 208. To find out where to get vaccinated in and around the Mission, visit our Vaccination page.

Are hospitalizations “decoupled” from cases? Since September 15, hospitalizations have fluctuated in the 1960s, with intensive care patients between 20 and 26 years old. October 4, DPH reports that there was 67 covid hospitalizations, or approximately 7.7 per 100,000 (based on a population of 874,000). The DPH said it had “temporarily suspended our reports on hospitalizations and revolutionary deaths to conduct a thorough review of the quality and completeness of the data.” According to the CDC, there was 43 new admissions for the week ending October 5 (-14 percent of the previous week). For the week ending October 5, covid patients represented 3.48 percent of hospital beds (no change of the previous week) and 8.82 percent intensive care beds (no change of the previous week). As of Sept. 27, the CDC says that of the more than 183 million U.S. residents vaccinated, 22 115 patients with covid vaccine infection have been hospitalized or have died (although 17 percent death and 18 percent of hospitalizations had no symptoms of covid, or their hospitalization or death was unrelated to covid).



After showing San Francisco above 1, Covid R Estimate lowered its most recent R number from San Francisco to .96. He increased his current estimate of California’s R number to .92. The ensemble also lowered its average R number from San Francisco to .85 while maintaining its California average at .84. Only one model of the set shows an SF transmission rate greater than 1.

As of October 1, DPH cites data from the SF Unified School District claiming 353 covid infections in nearly 52,000 students and nearly 10,000 public school staff. In private, parish and charter schools, there were 127 cases involving nearly 22,500 students and nearly 5,000 staff. DPH also says that “the vast majority of these infections occur outside of schools” citing only 18 “Suspected transmissions to school”.



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Positivity rates are based on testing, but not all tests (like rapid home tests) are counted. While the number of tests counted by the City is down compared to last winter, many more tests were collected than last spring and summer.

Covid-related deaths in San Francisco are still difficult to quantify. DPH added 5 more deaths in September, bringing the Delta total (August and September) to 68 so far, and the cumulative number of covid-related deaths to 644. According to DPH, more than half of the deaths were in people over the age of 80, almost all of them over 60. Less than 3% had no known underlying condition. DPH has stopped reporting the vaccination status of covid-related deaths.

After showing San Francisco above 1, Covid R Estimate lowered its most recent R number from San Francisco to .96. He increased his current estimate of California’s R number to .92. The ensemble also lowered its average R number from San Francisco to .85 while maintaining its California average at .84. Only one model of the set shows an SF transmission rate greater than 1.

As of October 1, DPH cites data from the SF Unified School District claiming 353 covid infections in nearly 52,000 students and nearly 10,000 public school staff. In private, parish and charter schools, there were 127 cases involving nearly 22,500 students and nearly 5,000 staff. DPH also says that “the vast majority of these infections occur outside of schools” citing only 18 “Suspected transmissions to school”.



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As of September 30, whites had 1,060 new cases in the month, Asians 647, Latinx 551, Black 213, Multiracial 51, Pacific Islanders 35 and Native Americans 9 new cases.

Positivity rates are based on testing, but not all tests (like rapid home tests) are counted. While the number of tests counted by the City is down compared to last winter, many more tests were collected than last spring and summer.

Covid-related deaths in San Francisco are still difficult to quantify. DPH added 5 more deaths in September, bringing the Delta total (August and September) to 68 so far, and the cumulative number of covid-related deaths to 644. According to DPH, more than half of the deaths were in people over the age of 80, almost all of them over 60. Less than 3% had no known underlying condition. DPH has stopped reporting the vaccination status of covid-related deaths.

After showing San Francisco above 1, Covid R Estimate lowered its most recent R number from San Francisco to .96. He increased his current estimate of California’s R number to .92. The ensemble also lowered its average R number from San Francisco to .85 while maintaining its California average at .84. Only one model of the set shows an SF transmission rate greater than 1.

As of October 1, DPH cites data from the SF Unified School District claiming 353 covid infections in nearly 52,000 students and nearly 10,000 public school staff. In private, parish and charter schools, there were 127 cases involving nearly 22,500 students and nearly 5,000 staff. DPH also says that “the vast majority of these infections occur outside of schools” citing only 18 “Suspected transmissions to school”.



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DPH reports for the week ending September 30, the seven-day moving average of daily new cases in the city rose to 82, or about 9.4 new cases per day per 100,000 inhabitants (based on a population of 874,000). The 7-day average case rate among vaccinated residents was 7.8 per 100,000 fully vaccinated residents and for unvaccinated residents 15.1 per 100,000 unvaccinated inhabitants. The CDC, using slightly different numbers, rates community transmission in the city as “substantial“.

As of September 30, whites had 1,060 new cases in the month, Asians 647, Latinx 551, Black 213, Multiracial 51, Pacific Islanders 35 and Native Americans 9 new cases.

Positivity rates are based on testing, but not all tests (like rapid home tests) are counted. While the number of tests counted by the City is down compared to last winter, many more tests were collected than last spring and summer.

Covid-related deaths in San Francisco are still difficult to quantify. DPH added 5 more deaths in September, bringing the Delta total (August and September) to 68 so far, and the cumulative number of covid-related deaths to 644. According to DPH, more than half of the deaths were in people over the age of 80, almost all of them over 60. Less than 3% had no known underlying condition. DPH has stopped reporting the vaccination status of covid-related deaths.

After showing San Francisco above 1, Covid R Estimate lowered its most recent R number from San Francisco to .96. He increased his current estimate of California’s R number to .92. The ensemble also lowered its average R number from San Francisco to .85 while maintaining its California average at .84. Only one model of the set shows an SF transmission rate greater than 1.

As of October 1, DPH cites data from the SF Unified School District claiming 353 covid infections in nearly 52,000 students and nearly 10,000 public school staff. In private, parish and charter schools, there were 127 cases involving nearly 22,500 students and nearly 5,000 staff. DPH also says that “the vast majority of these infections occur outside of schools” citing only 18 “Suspected transmissions to school”.



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Between August 4 and October 3, DPH recorded 561 new cases at the Mission for a rate of 95 New cases per 10,000 inhabitants. During this period, DPH recorded 690 new cases at Bayview Hunters Point or 182 new cases per 10,000 inhabitants. At Seacliff there was 17 new cases among 2,507 residents.

DPH reports for the week ending September 30, the seven-day moving average of daily new cases in the city rose to 82, or about 9.4 new cases per day per 100,000 inhabitants (based on a population of 874,000). The 7-day average case rate among vaccinated residents was 7.8 per 100,000 fully vaccinated residents and for unvaccinated residents 15.1 per 100,000 unvaccinated inhabitants. The CDC, using slightly different numbers, rates community transmission in the city as “substantial“.

As of September 30, whites had 1,060 new cases in the month, Asians 647, Latinx 551, Black 213, Multiracial 51, Pacific Islanders 35 and Native Americans 9 new cases.

Positivity rates are based on testing, but not all tests (like rapid home tests) are counted. While the number of tests counted by the City is down compared to last winter, many more tests were collected than last spring and summer.

Covid-related deaths in San Francisco are still difficult to quantify. DPH added 5 more deaths in September, bringing the Delta total (August and September) to 68 so far, and the cumulative number of covid-related deaths to 644. According to DPH, more than half of the deaths were in people over the age of 80, almost all of them over 60. Less than 3% had no known underlying condition. DPH has stopped reporting the vaccination status of covid-related deaths.

After showing San Francisco above 1, Covid R Estimate lowered its most recent R number from San Francisco to .96. He increased his current estimate of California’s R number to .92. The ensemble also lowered its average R number from San Francisco to .85 while maintaining its California average at .84. Only one model of the set shows an SF transmission rate greater than 1.

As of October 1, DPH cites data from the SF Unified School District claiming 353 covid infections in nearly 52,000 students and nearly 10,000 public school staff. In private, parish and charter schools, there were 127 cases involving nearly 22,500 students and nearly 5,000 staff. DPH also says that “the vast majority of these infections occur outside of schools” citing only 18 “Suspected transmissions to school”.



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The latest report from the Federal Department of Health and Human Services shows that the Zuckerberg San Francisco General Hospital 8 patients with covid and 9 intensive care beds available, while throughout the mission the CPMC had 4 patients with covid and 4 Intensive care beds available. Of 72 reported covid patients, 40 were at SFGH or UCSF, and at least 71 Intensive care beds available from reporting hospitals. California DPH says there is 83 Intensive care beds available in San Francisco. The SF DPH won’t say it.


Between August 4 and October 3, DPH recorded 561 new cases at the Mission for a rate of 95 New cases per 10,000 inhabitants. During this period, DPH recorded 690 new cases at Bayview Hunters Point or 182 new cases per 10,000 inhabitants. At Seacliff there was 17 new cases among 2,507 residents.

DPH reports for the week ending September 30, the seven-day moving average of daily new cases in the city rose to 82, or about 9.4 new cases per day per 100,000 inhabitants (based on a population of 874,000). The 7-day average case rate among vaccinated residents was 7.8 per 100,000 fully vaccinated residents and for unvaccinated residents 15.1 per 100,000 unvaccinated inhabitants. The CDC, using slightly different numbers, rates community transmission in the city as “substantial“.

As of September 30, whites had 1,060 new cases in the month, Asians 647, Latinx 551, Black 213, Multiracial 51, Pacific Islanders 35 and Native Americans 9 new cases.

Positivity rates are based on testing, but not all tests (like rapid home tests) are counted. While the number of tests counted by the City is down compared to last winter, many more tests were collected than last spring and summer.

Covid-related deaths in San Francisco are still difficult to quantify. DPH added 5 more deaths in September, bringing the Delta total (August and September) to 68 so far, and the cumulative number of covid-related deaths to 644. According to DPH, more than half of the deaths were in people over the age of 80, almost all of them over 60. Less than 3% had no known underlying condition. DPH has stopped reporting the vaccination status of covid-related deaths.

After showing San Francisco above 1, Covid R Estimate lowered its most recent R number from San Francisco to .96. He increased his current estimate of California’s R number to .92. The ensemble also lowered its average R number from San Francisco to .85 while maintaining its California average at .84. Only one model of the set shows an SF transmission rate greater than 1.

As of October 1, DPH cites data from the SF Unified School District claiming 353 covid infections in nearly 52,000 students and nearly 10,000 public school staff. In private, parish and charter schools, there were 127 cases involving nearly 22,500 students and nearly 5,000 staff. DPH also says that “the vast majority of these infections occur outside of schools” citing only 18 “Suspected transmissions to school”.



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