Implementation of California COVIDNet - a multi-sector collaboration for statewide SARS-CoV-2 genomic surveillance

Introduction

The SARS-CoV-2 pandemic represented a formidable scientific and technological challenge to public health due to its rapid spread and evolution. To meet these challenges and to characterize the virus over time, the State of California established the California SARS-CoV-2 Whole Genome Sequencing (WGS) Initiative, or "California COVIDNet". This initiative constituted an unprecedented multi-sector collaborative effort to achieve large-scale genomic surveillance of SARS-CoV-2 across California to monitor the spread of variants within the state, to detect new and emerging variants, and to characterize outbreaks in congregate, workplace, and other settings.

Methods

California COVIDNet consists of 50 laboratory partners that include public health laboratories, private clinical diagnostic laboratories, and academic sequencing facilities as well as expert advisors, scientists, consultants, and contractors. Data management, sample sourcing and processing, and computational infrastructure were major challenges that had to be resolved in the midst of the pandemic chaos in order to conduct SARS-CoV-2 genomic surveillance. Data management, storage, and analytics needs were addressed with both conventional database applications and newer cloud-based data solutions, which also fulfilled computational requirements.

Results

Representative and randomly selected samples were sourced from state-sponsored community testing sites. Since March of 2021, California COVIDNet partners have contributed more than 450,000 SARS-CoV-2 genomes sequenced from remnant samples from both molecular and antigen tests. Combined with genomes from CDC-contracted WGS labs, there are currently nearly 800,000 genomes from all 61 local health jurisdictions (LHJs) in California in the COVIDNet sequence database. More than 5% of all reported positive tests in the state have been sequenced, with similar rates of sequencing across 5 major geographic regions in the state.

Discussion

Implementation of California COVIDNet revealed challenges and limitations in the public health system. These were overcome by engaging in novel partnerships that established a successful genomic surveillance program which provided valuable data to inform the COVID-19 public health response in California. Significantly, California COVIDNet has provided a foundational data framework and computational infrastructure needed to respond to future public health crises.

Challenges with controlling varicella in prison settings: experience of California, 2010 to 2011

This article describes the epidemiology of varicella in one state prison in California during 2010 and 2011, control measures implemented, and associated costs. Eleven varicella cases were reported, of which nine were associated with two outbreaks. One outbreak consisted of three cases and the second consisted of six cases with two generations of spread. Among exposed inmates serologically tested, 98% (643/656) were varicella-zoster virus seropositive. The outbreaks resulted in > 1,000 inmates exposed, 444 staff exposures, and > $160,000 in costs. The authors documented the challenges and costs associated with controlling and managing varicella in a prison setting. A screening policy for evidence of varicella immunity for incoming inmates and staff and vaccination of susceptible persons has the potential to mitigate the impact of future outbreaks and reduce resources necessary to manage cases and outbreaks.

Abused and neglected children in court: knowledge and attitudes

OBJECTIVE

After maltreated children are taken into protective custody, dependency courts determine the children's placements. Many, if not most, maltreated children never attend their dependency court hearings. We had the rare opportunity to interview children in a jurisdiction where children regularly attend their detention hearings in dependency court. Our main goals were to assess maltreated children's knowledge and attitudes about their court experiences and identify predictors thereof. We also examined if the maltreated children desired greater participation in dependency court decisions.

METHODS

Immediately after attending their dependency court hearings, 7- to 10-year-olds were interviewed about their knowledge of, attitudes concerning, and participation in dependency court. Information was also extracted from the children's dependency court files.

RESULTS

Lack of understanding and negative attitudes were common. Age predicted court knowledge, and age, anxiety, court knowledge, abuse type, and criminal court referral predicted attitudes. Qualitative findings included that a substantial minority of children did not feel believed or listened to, and most children wanted to return home.

CONCLUSIONS

This research is relevant to current debates about the extent to which children should be involved in legal decisions. The results suggest that maltreated children may profit from greater understanding of dependency court. Moreover, the findings indicate that children often wish to have greater influence in dependency court decisions.

POLICY IMPLICATIONS

Professionals should consider providing children involved in dependency court hearings with age-appropriate information about the legal proceedings. Children may also benefit in dependency hearings from the opportunity, directly or indirectly (through their attorneys), to give voice to their wishes and needs.

Unemployment among women: examining the relationship of physical and psychological intimate partner violence and posttraumatic stress disorder

Prior research has demonstrated that intimate partner violence (IPV) is associated with employment instability among poor women. The current study assesses the broader relationship between IPV and women's workforce participation in a population-based sample of 6,698 California women. We examined past-year IPV by analyzing specific effects of physical violence, psychological violence, and posttraumatic stress disorder (PTSD) symptoms as predictors of unemployment. Results indicated substantial rates of unemployment among women who reported IPV, with rates of 20% among women who experienced psychological violence, 18% among women who experienced physical violence, and 19% among women with PTSD symptoms. When the relationship was adjusted for demographic characteristics and educational attainment, PTSD (adjusted odds ratio [AOR] = 1.60; 95% confidence interval [CI] = 1.22, 2.09) and psychological violence (AOR = 1.78; 95% CI = 1.36, 2.32), but not physical violence, were associated with unemployment. Implications for supported employment programs and workplace responses to IPV are discussed.

The relationship between child abuse and adult obesity among california women

BACKGROUND

Despite clinical studies suggesting that child abuse is associated with adult obesity, very few studies have been conducted with large community or state-based samples. This study examines the relationship between child abuse and adult obesity, relative to other risk factors such as demographics, food insecurity, inadequate fruit and vegetable consumption, and physical inactivity, in a representative sample of California women.

METHODS

Data are from the California Women's Health Survey, a state-based, random-digit-dial annual probability survey of California women. Participants included 11,115 nonpregnant women aged 18 or older, who provided complete data for all study variables. The telephone interview included assessment of child abuse (abstracted from the Traumatic Stress Schedule), food insecurity, perceived stress, physical activity, fruit and vegetable consumption, height, and weight. Data were collected in 2002, 2003, and 2004, and analyzed in 2006.

RESULTS

Obese (body mass index [BMI] of 30 or higher) women were significantly more likely to report exposure to child abuse (odds ratio [OR]=1.32, 95% confidence interval [CI]=1.23-1.42). In a multivariate model adjusted for age, race/ethnicity, education, food insecurity, inadequate fruit and vegetable consumption, physical inactivity, and perceived stress, women exposed to child abuse remained significantly more likely to be obese than unexposed women (adjusted OR=1.27, 95% CI=1.13-1.40). The population-attributable fraction of obesity associated with any type of abuse was 4.5% (95% CI=2.28-6.55).

CONCLUSIONS

Exposure to child abuse is associated with adult obesity among California women, even accounting for other relevant variables. This supports the notion that child abuse and its sequelae may be important targets for public health intervention, particularly in subpopulations where the prevalence of child abuse is known to be high.

Epidemiology and consequences of women's revictimization

This study uses Kraemer's approach for nonrandom comorbidity to identify the parameters of revictimization among women, using a diverse, population-based sample. Participants (n = 11,056) are from the California Women's Health Survey. Women were asked about childhood and adult violence and current symptoms of posttraumatic stress disorder (PTSD), depression, and anxiety. Logistic regressions adjusted for age, ethnicity, education, and poverty indicate that women who experienced childhood physical or sexual abuse were 5.8 (95% confidence interval, 5.2-6.4) times more likely to experience adult physical or sexual victimization. Revictimization affected 12% of women, and these women were substantially more likely to report current symptoms of anxiety, depression, and PTSD than women exposed to violence only in childhood or only as an adult. Revictimization is a methodologically distinct concept and is a potent risk factor for adult mental health problems. Prevention should target women exposed to both physical and sexual assault.

Who is food-insecure in California? Findings from the California Women's Health Survey, 2004

Objective

To identify factors associated with food insecurity in California women.

Design

The California Women's Health Survey is an ongoing annual telephone survey that collects data about health-related attitudes and behaviours from a randomly selected sample of women. Food insecurity of the women was measured by a 6-item subset of the Food Security Module. Statistical procedures included chi-square tests, t-tests, logistic regression analysis and analysis of covariance.

Setting

California, USA.

Subjects

Four thousand and thirty-seven women (18 years or older).

Results

Prevalence of food insecurity was 25.7%. After controlling for income, factors associated with greater food insecurity were Hispanic or Black race/ethnicity; less than a 12th grade education; being unmarried; less than 55 years old; being Spanish-speaking; having spent less than half of one's life in the USA; sadness/depression; feeling overwhelmed; poor physical/mental health interfering with activities; and fair to poor general health. Among Food Stamp Program (FSP) participants, 71% were food-insecure. Among FSP-eligible women who had not applied for the programme, the prevalence of food insecurity was lower among women responding that they did not need food stamps than in women giving other reasons for not applying (23.9% vs. 66.9%, P < 0.001). Factors associated with food insecurity in FSP recipients included being unable to make food stamps last for 30 days, feeling overwhelmed, and having a birthplace in Mexico or Central America.

Conclusions

Along with several socio-economic variables, poor physical and mental health is associated with food insecurity. Whether food insecurity is a cause or effect of poor health remains in question.

Intimate partner violence and housing instability

BACKGROUND

The mental and physical health consequences of intimate partner violence (IPV) have been well established, yet little is known about the impact of violence on a woman's ability to obtain and maintain housing. This cross-sectional study examines the relationship between recent IPV and housing instability among a representative sample of California women. It is expected that women who have experienced IPV will be at increased risk for housing instability as evidenced by: (1) late rent or mortgage, (2) frequent moves because of difficulty obtaining affordable housing, and/or (3) without their own housing.

METHODS

Data were taken from the 2003 California Women's Health Survey, a population-based, random-digit-dial, annual probability survey of adult California women (N=3619). Logistic regressions were used to predict housing instability in the past 12 months, adjusting for the following covariates; age, race/ethnicity, education, poverty status, marital status, children in the household, and past year IPV.

RESULTS

In the multivariate model, age, race/ethnicity, marital status, poverty, and IPV were significant predictors of housing instability. After adjusting for all covariates, women who experienced IPV in the last year had almost four times the odds of reporting housing instability than women who did not experience IPV (adjusted odds ratio=3.98, 95% confidence interval: 2.94-5.39).

CONCLUSIONS

This study found that IPV was associated with housing instability among California women. Future prospective studies are needed to learn more about the nature and direction of the relationship between IPV and housing instability and the possible associated negative health consequences.

Exposure to child abuse and risk for mental health problems in women

Risk for adult mental health problems associated with child sexual, physical, or emotional abuse and multiple types of child abuse was examined. Logistic regression analyses were used to test study hypotheses in a population-based sample of women (N = 3,936). As expected, child sexual, physical, and emotional abuse were independently associated with increased risk for mental health problems. History of multiple types of child abuse was also associated with elevated risk for mental health problems. In particular, exposure to all three types of child abuse was linked to a 23-fold increase in risk for probable posttraumatic stress disorder (PTSD). Findings underscore relations between child emotional abuse and adult mental health problems and highlight the need for mental health services for survivors of multiple types of child abuse.

Access to specialty mental health services among women in California

OBJECTIVE

The Anderson behavioral model was used to investigate racial and ethnic disparities in access to specialty mental health services among women in California as well as factors that might account for such disparities.

METHODS

The study was a cross-sectional examination of a probability sample of 3,750 California women. The main indicators of access to services were perceived need, service seeking, and service use. Multivariate models were constructed that accounted for need and enabling and demographic variables.

RESULTS

Significant racial and ethnic variations in access to specialty mental health services were observed. African-American, Hispanic, and Asian women were significantly less likely to use specialty mental health services than white women. Multivariate analyses showed that Hispanic and Asian women were less likely than white women to report perceived need, even after frequent mental distress had been taken into account. Among women with perceived need, African-American and Asian women were less likely than white women to seek mental health services after differences in insurance status had been taken into account. Among women who sought services, Hispanic women were less likely than white women to obtain services after adjustment for the effects of poverty. Need and enabling factors did not entirely account for the observed disparities in access to services.

CONCLUSIONS

Additional research is needed to identify gender- and culture-specific models for access to mental health services in order to decrease disparities in access. Factors such as perceived need and decisions to seek services are important factors that should be emphasized in future studies.

Contraceptive use and risk of unintended pregnancy in California

California is home to more than one out of eight American women of reproductive age. Because California has a large, diverse and growing population, national statistics do not necessarily describe the reproductive health of California women. This article presents risk for pregnancy and sexually transmitted infections among women in California based on the California Women's Health Survey. Over 8900 women of reproductive age who participated in this survey between 1998 and 2001 provide estimates of access to care and use of family-planning methods in the state. We find that 49% of the female population aged 18-44 in California is at risk of unintended pregnancy. Nine percent (9%) of women at risk of an unintended pregnancy are not using any method of contraception, primarily for method-related reasons, such as a concern about side effects or a dislike of available contraceptive methods. Among women at risk for unintended pregnancy, we find disparities by race/ethnicity and education in use of contraceptive methods.

Developmental and reproductive toxicity of inorganic arsenic: animal studies and human concerns

Information on the reproductive and developmental toxicity of inorganic arsenic is available primarily from studies in animals using arsenite and arsenate salts and arsenic trioxide. Inorganic arsenic has been extensively studied as a teratogen in animals. Data from animal studies demonstrate that arsenic can produce developmental toxicity, including malformation, death, and growth retardation, in four species (hamsters, mice, rats, rabbits). A characteristic pattern of malformations is produced, and the developmental toxicity effects are dependent on dose, route, and the day of gestation when exposure occurs. Studies with gavage and diet administration indicate that death and growth retardation are produced by oral arsenic exposure. Arsenic is readily transferred to the fetus and produces developmental toxicity in embryo culture. Animal studies have not identified an effect of arsenic on fertility in males or females. When females were dosed chronically for periods that included pregnancy, the primary effect of arsenic on reproduction was a dose-dependent increase in conceptus mortality and in postnatal growth retardation. Human data are limited to a few studies of populations exposed to arsenic from drinking water or from working at or living near smelters. Associations with spontaneous abortion and stillbirth have been reported in more than one of these studies, but interpretation of these studies is complicated because study populations were exposed to multiple chemicals. Thus, animal studies suggest that environmental arsenic exposures are primarily a risk to the developing fetus. In order to understand the implications for humans, attention must be given to comparative pharmacokinetics and metabolism, likely exposure scenarios, possible mechanisms of action, and the potential role of arsenic as an essential nutrient.

Management of pelvic inflammatory disease by primary care physicians. A comparison with Centers for Disease Control and Prevention guidelines

BACKGROUND

The Centers for Disease Control and Prevention published recommendations for clinicians on the management of pelvic inflammatory disease, but it is unknown if providers are aware of the guidelines or follow them.

GOAL

To compare pelvic inflammatory disease screening, diagnosis, treatment, and reporting practices among primary care physicians with the Centers for Disease Control and Prevention guidelines for pelvic inflammatory disease.

STUDY DESIGN

A weighted random sample of California primary care physicians surveyed in November 1992 and January 1993.

RESULTS

Of the 1,165 physicians surveyed, 553 (48%) returned completed questionnaires. Among respondents, 302 (55%) reported having treated a case of pelvic inflammatory disease during the last 12 months, and of these, 52% answered that they were unsure of or do not follow the Centers for Disease Control and Prevention guidelines for pelvic inflammatory disease. Pediatricians and those with more years since residency were less likely to deviate from the Centers for Disease Control and Prevention guidelines for pelvic inflammatory disease, and family practitioners were more likely to deviate from the guidelines.

CONCLUSIONS

Pelvic inflammatory disease is commonly encountered by primary care physicians in California. Training and experience were important predictors of compliance with the Centers for Disease Control and Prevention recommendations; however, substantial divergence from the guidelines occurs.

Cytokine expression of macrophages in HIV-1-associated vacuolar myelopathy

Macrophages are frequently present within the periaxonal and intramyelinic vacuoles that are located primarily in the posterior and lateral funiculi of the thoracic spinal cord in HIV-associated vacuolar myelopathy. But the role of these macrophages in the formation of the vacuoles is unclear. One hypothesis is that cytokines, such as interleukin-1 (IL-1) and tumor necrosis factor (TNF)-alpha, are produced locally by macrophages and have toxic effects on myelin or oligodendrocytes. The resulting myelin damage eventually culminates in the removal of myelin by macrophages and vacuole formation. We studied thoracic spinal cord specimens taken at autopsy from HIV-positive (+) and HIV-negative individuals. The predominant mononuclear cells present in HIV+ spinal cords are macrophages. They are located primarily in the posterior and lateral funiculi regardless of the presence or absence of vacuolar myelopathy. Macrophages and microglia are more frequent in HIV+ than HIV-negative individuals and these cells frequently stain for class I and class II antigens, IL-1, and TNF-alpha. Activated macrophages positive for IL-1 and TNF-alpha are great increased in the posterior and lateral funiculi of HIV+ individuals with and without vacuolar myelopathy, suggesting they are present prior to the development of vacuoles. Cytokines, such as TNF-alpha, may be toxic for myelin or oligodendrocytes, leading to myelin damage and removal by macrophages and vacuole formation.