San Francisco's Citywide COVID-19 Response: Strategies to Reduce COVID-19 Severity and Health Disparities, March 2020 Through May 2022.

San Francisco implemented one of the most intensive, comprehensive, multipronged COVID-19 pandemic responses in the United States using 4 core strategies: (1) aggressive mitigation measures to protect populations at risk for severe disease, (2) prioritization of resources in neighborhoods highly affected by COVID-19, (3) timely and adaptive data-driven policy making, and (4) leveraging of partnerships and public trust. We collected data to describe programmatic and population-level outcomes. The excess all-cause mortality rate in 2020 in San Francisco was half that seen in 2019 in California as a whole (8% vs 16%). In almost all age and race and ethnicity groups, excess mortality from COVID-19 was lower in San Francisco than in California overall, with markedly diminished excess mortality among people aged >65 years. The COVID-19 response in San Francisco highlights crucial lessons, particularly the importance of community responsiveness, joint planning, and collective action, to inform future pandemic response and advance health equity.

Factors Influencing Parent and Guardian Decisions on Vaccinating Their Children Against SARS-CoV-2: A Qualitative Study.

This qualitative analysis sought to explore factors that influenced parent/guardian intentions to vaccinate their children against SARS-CoV-2 in San Francisco, California, USA in order to inform San Francisco Department of Public Health's (SFDPH) youth vaccine rollout program. 30-minute, semi-structured telephone interviews were conducted with parents and guardians in either Spanish or English. Respondents shared their perspectives on vaccinating their children against SARS-CoV-2. Interviews were conducted over the telephone and recorded on Zoom. Participants (n = 40) were parents/guardians responding on behalf of their adolescent children (age 13+) and parents/guardians identified from the SFDPH COVID-19 testing database who tested for SARS-CoV-2 within the last 2 weeks. Interviews were conducted, audio recorded, transcribed, translated into English as appropriate, and rapidly analyzed in REDCap according to matrix analysis methodology to develop parent study themes. Perspectives on child vaccination were then explored through thematic analysis. Three themes were identified from the thematic analysis: (1) parental desires for children to return to school safely, (2) unclear messaging and information on COVID-19 prevention and vaccination, and (3) consideration of child's desires or opinions on receiving the vaccine. This study highlights specific factors influencing parent/guardian decisions on whether to vaccinate their children against SARS-CoV-2. The analysis also illustrates a potential role for children to play in influencing household vaccine decision-making.

Outdoor Activities Associated with Lower Odds of SARS-CoV-2 Acquisition: A Case-Control Study.

Access to recreational physical activities, particularly in outdoor spaces, has been a crucial outlet for physical and mental health during the COVID-19 pandemic. There is a need to understand how conducting these activities modulates the risk of SARS-CoV-2 infection. In this case-control study of unvaccinated individuals conducted in San Francisco, California, the odds of testing positive to SARS-CoV-2 were lower for those who conducted physical activity in outdoor locations (adjusted odds ratio [aOR]: 0.16, 95% confidence interval [CI]: 0.05, 0.40) in the two weeks prior to testing than for those who conducted no activity or indoor physical activity only. Individuals who visited outdoor parks, beaches, or playgrounds also had lower odds of testing positive to SARS-CoV-2 (aOR: 0.28, 95% CI: 0.11, 0.68) as compared with those who did not visit outdoor parks, beaches, or playgrounds. These findings, albeit in an unvaccinated population, offer observational data to support pre-existing ecological studies that suggest that activity in outdoor spaces lowers COVID-19 risk.

Evaluating the Impact of Language Concordance on Coronavirus Disease 2019 Contact Tracing Outcomes Among Spanish-Speaking Adults in San Francisco Between June and November 2020.

We evaluated the impact of language concordance-clinician or public health worker fluency in a patient's primary language-on coronavirus disease 2019 (COVID-19) contact tracing outcomes among 2668 Spanish-speaking adults in San Francisco. Language concordance was associated with 20% greater odds of COVID-19 testing and 53% greater odds of support service referrals.

Informatics response to address the COVID-19 pandemic in a safety net healthcare system.

In service of particularly vulnerable populations, safety net healthcare systems must nimbly leverage health information technology (IT), including electronic health records (EHRs), to coordinate the medical and public health response to the novel coronavirus (COVID-19). Six months after the San Francisco Department of Public Health implemented a new EHR across its hospitals and citywide clinics, California declared a state of emergency in response to COVID-19. This paper describes how the IT and informatics teams supported San Francisco Department of Public Health's goals of expanding the safety net healthcare system capacity, meeting the needs of specific vulnerable populations, increasing equity in COVID-19 testing access, and expanding public health analytics and research capacity. Key enabling factors included critical partnerships with operational leaders, early identification of priorities, a clear governance structure, agility in the face of rapidly changing circumstances, and a commitment to vulnerable populations.

The SARS-CoV-2 pandemic: the race to trace: contact tracing scale-up in San Francisco-early lessons learned.

In order to effectively control spread of coronavirus 2019 (COVID-19), it is essential that jurisdictions have the capacity to rapidly trace close contacts of each and every case. Best practice guidance on how to implement such programs is urgently needed. We describe the early experience in the City and County of San Francisco (CCSF), where the City's Department of Health expanded contact tracing capability in anticipation of changes in San Francisco's 'shelter in place' order between April and June 2020. Important prerequisites to successful scale-up included a rapid expansion of the COVID-19 response workforce, expansion of testing capability, and other containment resources. San Francisco's scale-up offers a model for how other jurisdictions can rapidly mobilize a workforce. We underscore the importance of an efficient digital case management system, effective training, and expansion of supportive service programs for those in quarantine or isolation, and metrics to ensure continuous performance improvement.

COVID-19 Susceptibility and Outcomes Among People Living With HIV in San Francisco.

INTRODUCTION: Studies to examine whether HIV predisposes to a higher incidence of COVID-19 or more severe disease are accumulating. Initial studies from New York City suggested more severe disease among people living with HIV (PLWH), but this was during a time when hospitals were over-capacity and health systems stretched. This report presents the incidence and outcomes among PLWH with COVID-19 in San Francisco over the first 6 months of the pandemic. METHODS: Community transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first reported in San Francisco on March 5, 2020. This report examines the match of the San Francisco Department of Public Health COVID-19 testing database and the San Francisco Department of Public Health HIV Surveillance case registry from March 24, 2020, to September 3, 2020. RESULTS: Among 4252 COVID-19 tests performed among PLWH, 4.5% (N = 193) were positive for COVID-19, compared with a 3.5% (N = 9626) positivity rate among the 272,555 people without HIV tested for COVID-19 (P < 0.001). The mean age of those infected with HIV/COVID-19 was 48 years (20-76), 38.9% White, 38.3% Latinx, 11.9% Black, and 91.2% were men. Only 54.6% of coinfected PLWH were housed, with the remainder marginally housed. The rate of severe illness with COVID-19 was not increased among PLWH. DISCUSSION: In San Francisco, susceptibility to COVID-19 was increased among PLWH over the first 6 months of the pandemic, although clinical outcomes were similar to those without HIV. Homelessness and higher rates of congregate living situations among PLWH likely accounted for this disparity. Special efforts to house patients with marginal housing during the COVID-19 pandemic are needed.

Measles transmission during a large outbreak in California.

A large measles outbreak in 2014-2015, linked to Disneyland theme parks, attracted international attention, and led to changes in California vaccine policy. We use dates of symptom onset and known epidemic links for California cases in this outbreak to estimate time-varying transmission in the outbreak, and to estimate generation membership of cases probabilistically. We find that transmission declined significantly during the course of the outbreak (p = 0.012), despite also finding that estimates of transmission rate by day or by generation can overestimate temporal decline. We additionally find that the outbreak size and duration alone are sufficient in this case to distinguish temporal decline from time-invariant transmission (p = 0.014). As use of a single large outbreak can lead to underestimates of immunity, however, we urge caution in interpretation of quantities estimated from this outbreak alone. Further research is needed to distinguish causes of temporal decline in transmission rates.

Relapse of Juvenile Idiopathic Arthritis-Associated Uveitis after Discontinuation of Immunomodulatory Therapy.

Purpose: To assess treatment outcomes in juvenile idiopathic arthritis (JIA)-associated uveitis and relapse rates upon discontinuation of immunomodulatory therapy (IMT). Methods: Medical records of patients with JIA-associated uveitis seen at the University of Illinois at Chicago and the F.I. Proctor Foundation uveitis clinics from September 14, 1988 to January 5, 2011 were reviewed. The main outcome was time to relapse after attempting to discontinue IMT.Results: Of 66 patients with JIA-associated uveitis, 51 (77%) received IMT as either sole or combination therapy. Of a total of 51, 41 (80%) patients achieved corticosteroid-sparing control. Attempts were made to discontinue treatment in 19/51 (37%) patients. Of a total of 19 patients, 13 (68%) attempting to discontinue IMT relapsed, with a median time to relapse of 288 days from the time of attempted taper/discontinuation (IQR: 108-338).Conclusions: Corticosteroid-sparing control of inflammation was achieved in the majority of patients; however, attempts to stop IMT were often unsuccessful. Close follow-up of patients after discontinuation of therapy is warranted.

Genotype-Specific Measles Transmissibility: A Branching Process Analysis.

Background: Substantial heterogeneity in measles outbreak sizes may be due to genotype-specific transmissibility. Using a branching process analysis, we characterize differences in measles transmission by estimating the association between genotype and the reproduction number R among postelimination California measles cases during 2000-2015 (400 cases, 165 outbreaks). Methods: Assuming a negative binomial secondary case distribution, we fit a branching process model to the distribution of outbreak sizes using maximum likelihood and estimated the reproduction number R for a multigenotype model. Results: Genotype B3 is found to be significantly more transmissible than other genotypes (P = .01) with an R of 0.64 (95% confidence interval [CI], .48-.71), while the R for all other genotypes combined is 0.43 (95% CI, .28-.54). This result is robust to excluding the 2014-2015 outbreak linked to Disneyland theme parks (referred to as "outbreak A" for conciseness and clarity) (P = .04) and modeling genotype as a random effect (P = .004 including outbreak A and P = .02 excluding outbreak A). This result was not accounted for by season of introduction, age of index case, or vaccination of the index case. The R for outbreaks with a school-aged index case is 0.69 (95% CI, .52-.78), while the R for outbreaks with a non-school-aged index case is 0.28 (95% CI, .19-.35), but this cannot account for differences between genotypes. Conclusions: Variability in measles transmissibility may have important implications for measles control; the vaccination threshold required for elimination may not be the same for all genotypes or age groups.

The impact of BMI on non-malignant respiratory symptoms and lung function in arsenic exposed adults of Northern Chile.

BACKGROUND: Elevated body mass index (BMI) and arsenic are both associated with cancer and with non-malignant lung disease. Using a unique exposure situation in Northern Chile with data on lifetime arsenic exposure, we previously identified the first evidence of an interaction between arsenic and BMI for the development of lung cancer. OBJECTIVES: We examined whether there was an interaction between arsenic and BMI for the development of non-malignant lung disease. METHODS: Data on lifetime arsenic exposure, respiratory symptoms, spirometry, BMI, and smoking were collected from 751 participants from cities in Northern Chile with varying levels of arsenic water concentrations. Spirometry values and respiratory symptoms were compared across subjects in different categories of arsenic exposure and BMI. RESULTS: Adults with both a BMI above the 90th percentile (>33.9kg/m2) and arsenic water concentrations ≥11µg/L exhibited high odds ratios (ORs) for cough (OR = 10.7, 95% confidence interval (CI): 3.03, 50.1), shortness of breath (OR = 14.2, 95% CI: 4.79, 52.4), wheeze (OR = 14.4, 95% CI: 4.80, 53.7), and the combined presence of any respiratory symptom (OR = 9.82, 95% CI: 4.22, 24.5). In subjects with lower BMIs, respiratory symptom ORs for arsenic water concentrations ≥11µg/L were markedly lower. In never-smokers, reductions in forced vital capacity associated with arsenic increased as BMI increased. Analysis of the FEV1/FVC ratio in never-smokers significantly increased as BMI and arsenic concentrations increased. Similar trends were not observed for FEV1 alone or in ever-smokers. CONCLUSIONS: This study provides preliminary evidence that BMI may increase the risk for arsenic-related non-malignant respiratory disease.

Clinical Presentation and Outcomes among Children with Sepsis Presenting to a Public Tertiary Hospital in Tanzania.

BACKGROUND: Pediatric sepsis causes significant global morbidity and mortality and low- and middle-income countries (LMICs) bear the bulk of the burden. International sepsis guidelines may not be relevant in LMICs, especially in sub-Saharan Africa (SSA), due to resource constraints and population differences. There is a critical lack of pediatric sepsis data from SSA, without which accurate risk stratification tools and context-appropriate, evidence-based protocols cannot be developed. The study's objectives were to characterize pediatric sepsis presentations, interventions, and outcomes in a public Emergency Medicine Department (EMD) in Tanzania. METHODS: Prospective descriptive study of children (28 days to 14 years) with sepsis [suspected infection with ≥2 clinical systemic inflammatory response syndrome (SIRS) criteria] presenting to a tertiary EMD in Dar es Salaam, Tanzania (July 1 to September 30, 2016). Outcomes included: in-hospital mortality (primary), EMD mortality, and hospital length of stay. We report descriptive statistics using means and SDs, medians and interquartile ranges, and counts and percentages as appropriate. Predictive abilities of SIRS criteria, the Alert-Verbal-Painful-Unresponsive (AVPU) score and the Lambaréné Organ Dysfunction Score (LODS) for in-hospital, early and late mortality were tested. RESULTS: Of the 2,232 children screened, 433 (19.4%) met inclusion criteria, and 405 were enrolled. There were 247 (61%) subjects referred from an outside facility. Approximately half (54.1%) received antibiotics in the EMD, and some form of microbiologic culture was collected in 35.8% (n = 145) of subjects. In-hospital and EMD mortality were 14.2 and 1.5%, respectively, median time to death was 3 days (IQR 1-6), and median length of stay was 6 days (IQR 1-12). SIRS criteria, the AVPU score, and the LODS had low positive (17-27.1, 33.3-43.9, 18.3-55.6%, respectively) and high negative predictive values (88.6-89.8, 86.5-91.2, 86.8-90.5%, respectively) for in-hospital mortality. CONCLUSION: This pediatric sepsis cohort had high and early in-hospital mortality. Current criteria and tested clinical scores were inadequate for risk-stratification and mortality prediction in this population and setting. Pediatric sepsis management must take into account the local patient population, etiologies of sepsis, healthcare system, and resource availability. Only through studies such as this that generate regional data in LMICs can accurate risk stratification tools and context-appropriate, evidence-based guidelines be developed.

The Effect of Contact Investigations and Public Health Interventions in the Control and Prevention of Measles Transmission: A Simulation Study.

BACKGROUND: Measles cases continue to occur despite its elimination status in the United States. To control transmission, public health officials confirm the measles diagnosis, identify close contacts of infectious cases, deliver public health interventions (i.e., post-exposure prophylaxis) among those who are eligible, and follow-up with the close contacts to determine overall health outcomes. A stochastic network simulation of measles contact tracing was conducted using existing agent-based modeling software and a synthetic population with high levels of immunity in order to estimate the impact of different interventions in controlling measles transmission. METHODS AND FINDINGS: The synthetic population was created to simulate California`s population in terms of population demographics, household, workplace, school, and neighborhood characteristics using California Department of Finance 2010 census data. Parameters for the model were obtained from a review of the literature, California measles case surveillance data, and expert opinion. Eight different scenarios defined by the use of three different public health interventions were evaluated: (a) post-exposure measles, mumps, and rubella (MMR) vaccine, (b) post-exposure immune globulin (IG), and (c) voluntary isolation and home quarantine in the presence or absence of public health response delays. Voluntary isolation and home quarantine coupled with one or two other interventions had the greatest reduction in the number of secondary cases infected by the index case and the probability of escape situations (i.e., the outbreak continues after 90 days). CONCLUSIONS: Interrupting contact patterns via voluntary isolation and home quarantine are particularly important in reducing the number of secondary cases infected by the index case and the probability of uncontrolled outbreaks.

External Validation of the Liverpool Uveal Melanoma Prognosticator Online.

PURPOSE: To validate the Liverpool Uveal Melanoma Prognosticator Online (LUMPO) in a cohort of patients treated at the University of California-San Francisco (UCSF). METHODS: A retrospective chart review was performed of 390 patients treated between 2002 and 2007 for choroidal melanoma at UCSF. Similar patients (n = 1175) treated at the Liverpool Ocular Oncology Centre (LOOC) were included in the study. The data were analyzed using the model previously developed for LUMPO, an online prognostication tool combining multiple prognostic factors. Main outcome measures included all-cause mortality and melanoma-specific mortality. Reliability of the survival estimates in each group of patients was indicated by the C-indices of discrimination and Hosmer-Lemeshow test. RESULTS: Patients treated at UCSF tended to be younger with thicker tumors, and were more likely to receive proton beam radiotherapy as primary treatment compared to patients at LOOC. There were no significance differences with respect to ciliary body involvement, melanoma cytomorphology, and mitotic counts between the two groups. Death occurred in 140/390 (35%) patients from UCSF and 409/1175 (34%) patients from LOOC, with no difference in overall mortality by Kaplan-Meier analysis (log rank test, P = 0.503). For all-cause mortality and melanoma-specific mortality, the C-index of discrimination and Hosmer-Lemeshow test at 5 years after treatment indicated good discrimination performance of the model, with no statistically significant difference between observed and predicted survival. CONCLUSIONS: Despite differences between the two cohorts, external validation in patients treated at UCSF indicates that LUMPO estimated the all-cause and melanoma-specific mortality well.

Comparison of Surgical Outcome After Ahmed Valve Implantation for Patients With and Without Fluocinolone Intravitreal Implant (Retisert).

PURPOSE: To determine whether long-term, slow-release exposure to corticosteroids with Retisert promotes better surgical outcomes after Ahmed valve implantation. PATIENTS: This comparative retrospective cohort study included 17 study eyes (10 patients) with uncontrolled uveitis requiring Retisert and Ahmed implantation, and 55 control eyes (51 patients) with other types of medically uncontrolled glaucoma that only received Ahmed. MATERIALS AND METHODS: Main outcome measures were intraocular pressure (IOP), glaucoma eye drops per day, best-corrected visual acuity, early complications, and late complications at 1, 3, 6, and 12 months. Linear mixed effects models were used to model IOP, glaucoma drops per day, and visual acuity at 1 year after surgery. RESULTS: At 1 year, the study eyes had a mean IOP of 12.24, which was lower than that for control eyes at 15.17 (P=0.04). At 1 year, the average number of glaucoma eye drops used per day for study eyes was 1.4, which was lower than that for control eyes at 2.3 (P=0.03). At 1 year, there were no statistically significant differences in change in visual acuity, early complications, and late complications between study and control eyes. CONCLUSIONS: Patients who received a Retisert implantation had lower IOP and used fewer glaucoma eye drops compared with control eyes at 1-year post-Ahmed valve surgery. This study suggests that long-term, slow-release corticosteroid medication from Retisert (fluocinolone acetonide) may improve the surgical outcome for patients with an Ahmed valve implantation and/or Retisert helps control uveitis in patients with uveitic glaucoma receiving Ahmed valves.

Correction: Evaluating Subcriticality during the Ebola Epidemic in West Africa.

[This corrects the article DOI: 10.1371/journal.pone.0140651.].

The permuted locus trial--Well suited for emerging pathogens?

The recent Ebola virus epidemic was waning by the time stakeholders were ready to field vaccines for testing but an evidence-based response to a novel pathogen will surely be required again. Here, we present a design for such a randomized controlled trial. The permuted locus trial was originally intended for studying the influence of water wells on trachoma. While outcomes can be measured in individuals, neither individuals nor groups are themselves randomized to arms, just potential well-sites, or in the case of an epidemic, index cases. The permuted locus trial may be used when classic individual and cluster-randomized trial design and analyses may not be optimal.

Evaluating Subcriticality during the Ebola Epidemic in West Africa.

The 2014-2015 Ebola outbreak is the largest and most widespread to date. In order to estimate ongoing transmission in the affected countries, we estimated the weekly average number of secondary cases caused by one individual infected with Ebola throughout the infectious period for each affected West African country using a stochastic hidden Markov model fitted to case data from the World Health Organization. If the average number of infections caused by one Ebola infection is less than 1.0, the epidemic is subcritical and cannot sustain itself. The epidemics in Liberia and Sierra Leone have approached subcriticality at some point during the epidemic; the epidemic in Guinea is ongoing with no evidence that it is subcritical. Response efforts to control the epidemic should continue in order to eliminate Ebola cases in West Africa.