Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California's SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet.

The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did not have the infrastructure in place to handle the vast amount of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence data generated. The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet. While challenges remain for public health genomic surveillance worldwide, California COVIDNet serves as a framework for a scaled and successful bioinformatics infrastructure that has expanded beyond SARS-CoV-2 to other pathogens of public health importance.

COVID-19 Testing Strategies for K-12 Schools in California: A Cost-Effectiveness Analysis.

Public health officials must provide guidance on operating schools safely during the COVID-19 pandemic. Using data from April-December 2021, we conducted a cost-effectiveness analysis to assess six screening strategies for schools using SARS-CoV-2 antigen and PCR tests and varying screening frequencies for 1000 individuals. We estimated secondary infections averted, quality-adjusted life years (QALYs), cost per QALY gained, and unnecessary school days missed per infection averted. We conducted sensitivity analyses for the more transmissible Omicron variant. Weekly antigen testing with PCR follow-up for positives was the most cost-effective option given moderate transmission, adding 0.035 QALYs at a cost of USD 320,000 per QALY gained in the base case (Reff = 1.1, prevalence = 0.2%). This strategy had the fewest needlessly missed school days (ten) per secondary infection averted. During widespread community transmission with Omicron (Reff = 1.5, prevalence = 5.8%), twice weekly antigen testing with PCR follow-up led to 2.02 QALYs gained compared to no test and cost the least (USD 187,300), with 0.5 needlessly missed schooldays per infection averted. In periods of moderate community transmission, weekly antigen testing with PCR follow up can help reduce transmission in schools with minimal unnecessary days of school missed. During widespread community transmission, twice weekly antigen screening with PCR confirmation is the most cost-effective and efficient strategy. Schools may benefit from resources to implement routine asymptomatic testing during surges; benefits decline as community transmission declines.

Large-Scale Implementation of a Daily Rapid Antigen Testing Program in California for Detecting SARS-CoV-2.

Objectives. To evaluate a daily antigen testing program for health care personnel. Methods. We examined antigen testing results between December 13, 2020, and April 30, 2021, from 5 forensic psychiatric inpatient hospitals throughout California. Results. Among 471 023 antigen tests administered, 449 positives (0.0036% false positives) were detected. Conclusions. Antigen tests had low false-positive rates, high positive predictive value, and high levels of acceptability, important characteristics when considering their application in the community. Public Health Implications. Daily antigen testing was feasible and should be considered to reduce COVID-19 transmission. (Am J Public Health. 2022;112(3):467-471. https://doi.org/10.2105/AJPH.2021.306588).

Measuring the Impact of the COVID-19 Pandemic on Sexually Transmitted Diseases Public Health Surveillance and Program Operations in the State of California.

BACKGROUND: As public health personnel and resources are redirected to COVID-19, sexually transmitted diseases (STD) programs have been unable to sustain pre-COVID-19 activities. METHODS: We used California (CA) surveillance data to describe trends in case reporting for gonorrhea, chlamydia, and syphilis of any stage in the pre- versus post-COVID-19 eras (January-June 2019 and January-June 2020). We also analyzed data from an electronic survey administered by the CA STD Control Branch to local health jurisdictions in April, June, and September of 2020, assessing the impact of COVID-19 on STD programs. RESULTS: There were sharp declines in cases of all reportable bacterial STDs occurring in conjunction with the March 19, 2020 CA stay-at-home order, most of which did not return to baseline by July. Comparing January-June 2020 to January-June of 2019, there were decreases in reported cases of chlamydia (31%), late syphilis (19%), primary/secondary syphilis (15%), early nonprimary nonsecondary syphilis (14%), and gonorrhea (13%). The largest percentage declines in STD case reporting were among Hispanic, Asian/Pacific Islander, and Black persons. Seventy-eight percent of local health jurisdiction respondents indicated that half or more of their workforce had been redeployed to COVID-19 by September 2020. CONCLUSIONS: During the COVID-19 era, STD case reporting and programmatic functions have diminished throughout CA. Because this may contribute to decreases or delays in STD diagnosis and treatment-with resultant increases in STD transmission-providers and public health officials should prepare for potential increases in STD-related morbidity in the months and years to come.

Public Health Responses to COVID-19 Outbreaks on Cruise Ships - Worldwide, February-March 2020.

An estimated 30 million passengers are transported on 272 cruise ships worldwide each year* (1). Cruise ships bring diverse populations into proximity for many days, facilitating transmission of respiratory illness (2). SARS-CoV-2, the virus that causes coronavirus disease (COVID-19) was first identified in Wuhan, China, in December 2019 and has since spread worldwide to at least 187 countries and territories. Widespread COVID-19 transmission on cruise ships has been reported as well (3). Passengers on certain cruise ship voyages might be aged ≥65 years, which places them at greater risk for severe consequences of SARS-CoV-2 infection (4). During February-March 2020, COVID-19 outbreaks associated with three cruise ship voyages have caused more than 800 laboratory-confirmed cases among passengers and crew, including 10 deaths. Transmission occurred across multiple voyages of several ships. This report describes public health responses to COVID-19 outbreaks on these ships. COVID-19 on cruise ships poses a risk for rapid spread of disease, causing outbreaks in a vulnerable population, and aggressive efforts are required to contain spread. All persons should defer all cruise travel worldwide during the COVID-19 pandemic.