Community transmission of SARS-CoV-2 in San Francisco during lockdown

Jun 19 2020

Early this year, the COVID-19 outbreak began in the United States in a muted manner, simmering over a few weeks to emerge as a full-fledged epidemic in New York and other states. Now, a new study published on the preprint server medRxiv* in June 2020 reveals the pattern of community spread throughout the sheltering-in-place period in San Francisco.

SAN FRANCISCO, CA - May 24, 2020: Image Credit: Kevin McGovern / Shutterstock

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

Early Lockdown in San Francisco

Scientists now believe the virus was introduced to the U.S. not once but several times in the earliest weeks of 2020 in California to begin with. This state was also the first in the USA to make sheltering-in-place mandatory, on March 19, 2020. San Francisco, however, had already passed into a state of local emergency on February 25, 2020, with a progressively increasing set of restrictions on social gatherings, ending in the shelter-in-place mandate on March 16, 2020.

This is probably why even at the peak, the number of hospitalizations and deaths due to COVID-19 in April was only a tenth of that seen in the most hard-pressed cities like New York. However, the Latin and other people of color continue to be the worst-hit, with 45% of cases in San Francisco belonging to the Latinx community, which makes up only 15% of the population.

Community Testing: The Study

Nonetheless, the total estimate of community infection is many times higher than the number of hospital admissions and deaths. This number may be impossible to estimate at present due to the restriction of COVID-19 testing to symptomatic patients, for the most part. Moreover, diagnostic criteria have not changed, while the tests themselves are not uniform in performance. Worst of all, some of the communities most severely affected do not have access to easy testing.

The current study attempts to examine the nature and scope of community spread in a thickly populated segment of a Latinx community in San Francisco six weeks into the lockdown period. Called Unidos en Salud, the program offered free RT-PCR and antibody testing for all residents at or above the age of four years, and for those who worked in the same locality.

The region of testing covered 16 square blocks, or a tenth of a square mile, with about 5,000 residents, about 60% being Latinx and most of the remaining white. The median income is about $40,000 a year, but a third earn above $50,000 annually and a fifth above $200,000 a year.

Distribution of Positive Cases

The researchers succeeded in conducting almost 4,000 people, almost equally male and female, but only 40% Latinx and 40% White. The incidence of positive tests by PCR was 2% (83 people), while 3.4% were antibody-positive.

The distribution of PCR-positivity was 1.7% of residents, 6% of workers, and 1.6% of neighboring block residents. Among the 237 people tested with symptoms of COVID-19, only 31 tested positive by PCR.

Antibody tests were positive in 3% of residents, 2% of adjacent block residents, but 8% of workers. About 6% were estimated to have had the infection, overall, among the residents of the tract, with a quarter being recent and one-half prior infection.

Among the 2% who tested PCR-positive, 95% were Latinx, with a median age of 38 years, and 76% male. The point prevalence was 4% among Latinx vs. 0.2% among non-Latinx residents. For workers in the tested area, Latinx workers had a point prevalence of over 10% compared to 0 among non-Latinx workers.

The remaining analysis of risk factors for PCR-positivity was confined to the Latinx group, which showed that the odds of being positive were increased ninefold with annual income below $50,000, about 3.6-fold if they had contact with a COVID-19 patient, 2.6 times if they had a frontline job, and twice as high for males.

About 90% of recent infections occurred in households with income below $50,000. They were more likely to be Latinx, to have frontline jobs or unable to work from home, or unemployed, to live in a household earning below $50,000 a year, and to have three or more members in the household.

Impact of Socioeconomic Status

There were huge differences in the degree of risk for COVID-19 infection among people from different races and economic statuses. Latinx residents had a point prevalence almost 20 times higher than that of non-Latinx residents, and those recently infected were almost always those who had lower incomes, worked on the frontline, or were unemployed.

Antibody testing indicating prior infection was more widely distributed among various races and economic statuses. Recent PCR-positive individuals had higher viral titers, and most were asymptomatic at the time of testing. This shows that viral spread is active among certain segments of the population and if not urgently checked, could lead to a failure of containment.

The use of open-access testing across a whole community is fundamental to shape proper testing strategies and public health policies to reduce the impact of the outbreak and control measures. The current testing program shows that during a lockdown, economic factors led to the infection becoming concentrated among Latinx residents, mostly because they could not work their frontline jobs from home, nor could they maintain their income otherwise.

The family composition, with multiple generations sharing the home, often with multiple families in the same home, also drove the spread of the virus and reflects the steep increase in rental costs, impacting mostly the low-income group, again. These trends are mirrored in the differences in hospitalization and deaths due to COVID-19 across the nation as well.

Implications and Applications of the Study

The sequencing of the virus strains from this tract shows that the virus was introduced several times, and the majority of recent infections are due to working in the tract leading to the acquisition and subsequent spreading of the virus to family members in this densely populated area. Thus, this study does not support the idea that Latinx are intrinsically vulnerable to the infection, nor that the lack of adherence to lockdown norms is responsible for the spread. Neither does it allow the community to be termed a hotspot of community spread.

PCR and antibody testing is also proved to be crucial in identifying infection more accurately, even in asymptomatic individuals, who are also shown to have high viral titers.

The researchers point out several applications. First of all, there is a need to overcome the economic barriers to sheltering in place for low-income frontline worker communities. Secondly, community-led and targeted testing is essential. Job security and financial help for those who test positive are important parts of containing spread in this setting, as is sensitive contact tracing.

A positive offshoot of the study is the May 4, 2020, public announcement of free testing for all essential workers with or without symptoms, and on May 28, 2020, of the “Right to Recover” policy which pays low-income workers with COVID-19 during their self-isolation and quarantine period. More longitudinal studies will be required to help evaluate how effective these measures are over time, which will help shape public responses to the changing situation.

The study sums up: “Improving access to SARS-CoV-2 testing, regardless of symptoms, through community-led, low-barrier testing programs in vulnerable communities, coupled with economic support and protections for low-income workers during isolation and quarantine are urgently needed to reduce community transmission and address the massive disparities in SARS-CoV-2 infection observed in the U.S.”

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources