Immune escape and attenuated severity associated with the SARS-CoV-2 BA.2.86/JN.1 lineage

The SARS-CoV-2 BA.2.86 lineage, and its sublineage JN.1 in particular, achieved widespread transmission in the US during winter 2023-24. However, the increase in infections was not accompanied by increases in COVID-19 hospitalizations and mortality commensurate with prior waves. To understand shifts in COVID-19 epidemiology associated with JN.1 emergence, we compared characteristics and clinical outcomes of time-matched cases infected with BA.2.86- derived lineages (predominantly representing JN.1) versus co-circulating XBB-derived lineages in December, 2023 and January, 2024. Cases infected with BA.2.86-derived lineages received greater numbers of COVID-19 vaccine doses, including XBB.1.5-targeted and BA.4/BA.5-targeted boosters, in comparison to cases infected with XBB-derived lineages. Additionally, cases infected with BA.2.86-derived lineages experienced greater numbers of documented prior SARS-CoV-2 infections. These associations of BA.2.86-derived lineages with immune escape were confirmed when comparing cases diagnosed during periods when JN.1 was the predominant circulating lineage to cases diagnosed during November, 2023. Cases infected with BA.2.86-derived lineages, or during periods when JN.1 was the predominant circulating lineage, also experienced lower risk of progression to severe clinical outcomes requiring emergency department consultations or hospital admission. Sensitivity analyses suggested under-ascertainment of prior infections, even if differential between cases infected with BA.2.86-derived lineages and non-BA.2.86 lineages, could not explain this apparent attenuation of severity. Our findings implicate escape from immunity acquired from prior vaccination or infection in the emergence of the JN.1 lineage and suggest infections with this lineage are less likely to experience clinically-severe disease. Monitoring of immune escape and clinical severity in emerging SARS-CoV-2 variants remains a priority to inform responses.

Predictors of nirmatrelvir-ritonavir receipt among COVID-19 patients in a large US health system

A clear understanding of real-world uptake of nirmatrelvir-ritonavir for treatment of SARS-CoV-2 can inform treatment allocation strategies and improve interpretation of effectiveness studies. We used data from a large US healthcare system to describe nirmatrelvir-ritonavir dispenses among all SARS-CoV-2 positive patients aged ≥ 12 years meeting recommended National Institutes of Health treatment eligibility criteria for the study period between 1 January and 31 December, 2022. Overall, 10.9% (N = 34,791/319,900) of treatment eligible patients with SARS-CoV-2 infections received nirmatrelvir-ritonavir over the study period. Although uptake of nirmatrelvir-ritonavir increased over time, by the end of 2022, less than a quarter of treatment eligible patients with SARS-CoV-2 infections had received nirmatrelvir-ritonavir. Across patient demographics, treatment was generally consistent with tiered treatment guidelines, with dispenses concentrated among patients aged ≥ 65 years (14,706/63,921; 23.0%), and with multiple comorbidities (10,989/54,431; 20.1%). However, neighborhoods of lower socioeconomic status (upper third of neighborhood deprivation index [NDI]) had between 12% (95% CI: 7-18%) and 28% (25-32%) lower odds of treatment dispense over the time periods studied compared to the lower third of NDI distribution, even after accounting for demographic and clinical characteristics. A limited chart review (N = 40) confirmed that in some cases a decision not to treat was appropriate and aligned with national guidelines to use clinical judgement on a case-by-case basis. There is a need to enhance patient and provider awareness on the availability and benefits of nirmatrelvir-ritonavir for the treatment of COVID-19 illness.

Mortality risk after COVID-19 vaccination: A self-controlled case series study

BACKGROUND

Although previous studies found no-increased mortality risk after COVID-19 vaccination, residual confounding bias might have impacted the findings. Using a modified self-controlled case series (SCCS) design, we assessed the risk of non-COVID-19 mortality, all-cause mortality, and four cardiac-related death outcomes after primary series COVID-19 vaccination.

METHODS

We analyzed all deaths between December 14, 2020, and August 11, 2021, among individuals from eight Vaccine Safety Datalink sites. Demographic characteristics of deaths in recipients of COVID-19 vaccines and unvaccinated individuals were reported. We conducted SCCS analyses by vaccine type and death outcomes and reported relative incidences (RI). The observation period for death spanned from the dates of emergency use authorization to the end of the study period (August 11, 2021) without censoring the observation period upon death. We pre-specified a primary risk interval of 28-day and a secondary risk interval of 14-day after each vaccination dose. Adjusting for seasonality in mortality analyses is crucial because death rates vary over time. Deaths among unvaccinated individuals were included in SCCS analyses to account for seasonality by incorporating calendar month in the models.

RESULTS

For Pfizer-BioNTech (BNT162b2), RIs of non-COVID-19 mortality, all-cause mortality, and four cardiac-related death outcomes were below 1 and 95 % confidence intervals (CIs) excluded 1 across both doses and both risk intervals. For Moderna (mRNA-1273), RI point estimates of all outcomes were below 1, although the 95 % CIs of two RI estimates included 1: cardiac-related (RI = 0.78, 95 % CI, 0.58-1.04) and non-COVID-19 cardiac-related mortality (RI = 0.80, 95 % CI, 0.60-1.08) 14 days after the second dose in individuals without pre-existing cancer and heart disease. For Janssen (Ad26.COV2.S), RIs of four cardiac-related death outcomes ranged from 0.94 to 0.98 for the 14-day risk interval, and 0.68 to 0.72 for the 28-day risk interval and 95 % CIs included 1.

CONCLUSION

Using a modified SCCS design and adjusting for temporal trends, no-increased risk was found for non-COVID-19 mortality, all-cause mortality, and four cardiac-related death outcomes among recipients of the three COVID-19 vaccines used in the US.

Impact of the COVID-19 Pandemic on Health Care Utilization in the Vaccine Safety Datalink: Retrospective Cohort Study

BACKGROUND

Understanding the long-term impact of the COVID-19 pandemic on health care utilization is important to health care organizations and policy makers for strategic planning, as well as to researchers when designing studies that use observational electronic health record data during the pandemic period.

OBJECTIVE

This study aimed to evaluate the changes in health care utilization across all care settings among a large, diverse, and insured population in the United States during the COVID-19 pandemic.

METHODS

We conducted a retrospective cohort study within 8 health care organizations participating in the Vaccine Safety Datalink Project using electronic health record data from members of all ages from January 1, 2017, to December 31, 2021. The visit rates per person-year were calculated monthly during the study period for 4 health care settings combined as well as by inpatient, emergency department (ED), outpatient, and telehealth settings, both among all members and members without COVID-19. Difference-in-difference analysis and interrupted time series analysis were performed to assess the changes in visit rates from the prepandemic period (January 2017 to February 2020) to the early pandemic period (April-December 2020) and the later pandemic period (July-December 2021), respectively. An exploratory analysis was also conducted to assess trends through June 2023 at one of the largest sites, Kaiser Permanente Southern California.

RESULTS

The study included more than 11 million members from 2017 to 2021. Compared with the prepandemic period, we found reductions in visit rates during the early pandemic period for all in-person care settings. During the later pandemic period, overall use reached 8.36 visits per person-year, exceeding the prepandemic level of 7.49 visits per person-year in 2019 (adjusted percent change 5.1%, 95% CI 0.6%-9.9%); inpatient and ED visits returned to prepandemic levels among all members, although they remained low at 0.095 and 0.241 visits per person-year, indicating a 7.5% and 8% decrease compared to pre-pandemic levels among members without COVID-19, respectively. Telehealth visits, which were approximately 42% of the volume of outpatient visits during the later pandemic period, were increased by 97.5% (95% CI 86.0%-109.7%) from 0.865 visits per person-year in 2019 to 2.35 visits per person-year in the later pandemic period. The trends in Kaiser Permanente Southern California were similar to those of the entire study population. Visit rates from January 2022 to June 2023 were stable and appeared to be a continuation of the use levels observed at the end of 2021.

CONCLUSIONS

Telehealth services became a mainstay of the health care system during the late COVID-19 pandemic period. Inpatient and ED visits returned to prepandemic levels, although they remained low among members without evidence of COVID-19. Our findings provide valuable information for strategic resource allocation for postpandemic patient care and for designing observational studies involving the pandemic period.

Effectiveness of BNT162b2 BA.4/5 bivalent mRNA vaccine against a range of COVID-19 outcomes in a large health system in the USA: a test-negative case-control study

BACKGROUND

XBB-related omicron sublineages have recently replaced BA.4/5 as the predominant omicron sublineages in the USA and other regions globally. Despite preliminary signs of immune evasion of XBB sublineages, few data exist describing the real-world effectiveness of bivalent COVID-19 vaccines, especially against XBB-related illness. We aimed to investigate the effectiveness of the Pfizer--BioNTech BNT162b2 BA.4/5 bivalent vaccine against both BA.4/5-related and XBB-related disease in adults aged 18 years or older.

METHODS

In this test-negative case-control study, we estimated the effectiveness of the BNT162b2 BA.4/5 bivalent vaccine using data from electronic health records of Kaiser Permanente Southern California health system members aged 18 years or older who received at least two doses of the wild-type COVID-19 mRNA vaccines. Participants sought care for acute respiratory infection between Aug 31, 2022, and April 15, 2023, and were tested for SARS-CoV-2 via PCR tests. Relative vaccine effectiveness (≥2 doses of wild-type mRNA vaccine plus a BNT162b2 BA.4/5 bivalent booster vs ≥2 doses of a wild-type mRNA vaccine alone) and absolute vaccine effectiveness (vs unvaccinated individuals) was estimated against critical illness related to acute respiratory infection (intensive care unit [ICU] admission, mechanical ventilation, or inpatient death), hospital admission, emergency department or urgent care visits, and in-person outpatient encounters with odds ratios from logistic regression models adjusted for demographic and clinical factors. We stratified vaccine effectiveness estimates for hospital admission, emergency department or urgent care visits, and outpatient encounters by omicron sublineage (ie, likely BA.4/5-related vs likely XBB-related), time since bivalent booster receipt, age group, number of wild-type doses received, and immunocompromised status. This study is registered with ClinicalTrials.gov (NCT04848584).

FINDINGS

Analyses were conducted for 123 419 encounters (24 246 COVID-19 cases and 99 173 test-negative controls), including 4131 episode of critical illness (a subset of hospital admissions), 14 529 hospital admissions, 63 566 emergency department or urgent care visits, and 45 324 outpatient visits. 20 555 infections were BA.4/5 related and 3691 were XBB related. In adjusted analyses, relative vaccine effectiveness for those who received the BNT162b2 BA.4/5 bivalent booster compared with those who received at least two doses of a wild-type mRNA vaccine alone was an additional 50% (95% CI 23-68) against critical illness, an additional 39% (28-49) against hospital admission, an additional 35% (30-40) against emergency department or urgent care visits, and an additional 28% (22-33) against outpatient encounters. Waning of the bivalent booster from 0-3 months to 4-7 months after vaccination was evident for outpatient outcomes but was not detected for critical illness, hospital admission, and emergency department or urgent care outcomes. The relative effectiveness of the BNT162b2 BA.4/5 bivalent booster for XBB-related infections compared with BA.4/5-related infections was 56% (95% CI 12-78) versus 40% (27-50) for hospital admission; 34% (21-45) versus 36% (30-41) against emergency department or urgent care visits; and 29% (19-38) versus 27% (20-33) for outpatient encounters.

INTERPRETATION

By mid-April, 2023, individuals previously vaccinated only with wild-type vaccines had little protection against COVID-19-including hospital admission. A BNT162b2 BA.4/5 bivalent booster restored protection against a range of COVID-19 outcomes, including against XBB-related sublineages, with the most substantial protection observed against hospital admission and critical illness.

FUNDING

Pfizer.

Factors associated with uptake of bivalent mRNA COVID-19 vaccines in a large US health care system

BACKGROUND

Bivalent mRNA COVID-19 vaccines were developed to provide protection against the original SARS-CoV-2 strain and Omicron BA.4/BA.5 variants, but uptake in the United States has been low. Sociodemographic disparities in COVID-19 vaccine uptake have been documented, but it is unclear if similar disparities persist among individuals who previously completed a primary series of monovalent COVID-19 vaccine.

METHODS

We conducted a retrospective cohort study at Kaiser Permanente Southern California (KPSC) including youth aged 5-17 years and adults aged ≥18 years who were KPSC members and had completed a primary series of monovalent COVID-19 vaccine. Individuals were followed from index date (date of eligibility for bivalent vaccine) to 03/31/2023 to ascertain receipt of any dose of bivalent mRNA COVID-19 vaccine or until disenrollment from KPSC or death. Multivariable robust Poisson regression was conducted to assess the adjusted relative risk and 95 % confidence intervals of factors associated with receipt of bivalent vaccine.

RESULTS

The final cohorts included 305,339 youth and 2,534,619 adults, of whom 19.5 % and 30.7 %, respectively, had received bivalent COVID-19 vaccine. Factors associated with being more likely to receive bivalent COVID-19 vaccine included older age, Asian race, more prior year outpatient and virtual visits, Charlson score ≥1, and immunocompromised status. Factors associated with being less likely to receive a bivalent COVID-19 vaccine included age 12-17 vs 5-11 years, Hispanic and non-Hispanic Black race/ethnicity, ≥1 prior year inpatient or emergency department visits, prior history of SARS-CoV-2 infection (adults only), Medicaid insurance, and higher neighborhood deprivation index.

CONCLUSION

Even among youth and adults who had previously received a primary series of monovalent COVID-19 vaccine, sociodemographic and clinical disparities were observed in receipt of bivalent COVID-19 vaccine. These findings are critical to inform equitable strategies for the implementation of the updated monovalent COVID-19 vaccine targeting the Omicron XBB strain.

Burden of Lower Respiratory Tract Infections Preventable by Adult Immunization With 15- and 20-Valent Pneumococcal Conjugate Vaccines in the United States

BACKGROUND

Updated recommendations of the US Advisory Committee on Immunization Practices indicate that all adults aged ≥65 years and adults aged <65 years with comorbid conditions should receive 15- and 20-valent pneumococcal conjugate vaccines (PCV15/20). We aimed to assess the potential impact of these recommendations on the burden of lower respiratory tract infections (LRTIs) among adults.

METHODS

We estimated the incidence of LRTI cases and associated hospital admissions among enrollees of Kaiser Permanente Southern California from 2016 through 2019. We used a counterfactual inference framework to estimate excess LRTI-associated risk of death up to 180 days after diagnosis. We used prior estimates of PCV13 effectiveness against LRTI to model potential direct effects of PCV15/20 by age group and risk status.

RESULTS

Use of PCV15 and PCV20, respectively, could prevent 89.3 (95% confidence interval, 41.3-131.8) and 108.6 (50.4-159.1) medically attended LRTI cases; 21.9 (10.1-32.0) and 26.6 (12.4-38.7) hospitalized LRTI cases; and 7.1 (3.3-10.5) and 8.7 (4.0-12.7) excess LRTI-associated deaths, each per 10 000 person-years. Among at-risk adults aged <65 years, use of PCV15 and PCV20 could prevent 85.7 (39.6-131.5) and 102.7 (47.8-156.7) medically attended LRTI cases per 10 000 person-years; 5.1 (2.4-8.6) and 6.2 (2.8-10.2) LRTI hospitalizations per 10 000 person-years, and 0.9 (0.4-1.4) and 1.1 (0.5-1.7) excess LRTI-associated deaths per 10 000 person-years.

CONCLUSIONS

Our findings suggest recent recommendations, including PCV15/20 within adult pneumococcal vaccine series, may substantially reduce LRTI burden.

Real-World Evidence to Supplement Randomized Clinical Trials: Tocilizumab for Severe COVID-19 Pneumonia vs. a Cohort Receiving Standard of Care

Randomized controlled trials (RCTs) remain the gold standard for evaluating treatment efficacy, but real-world evidence can supplement RCT results. Tocilizumab was not found to reduce 28-day mortality in a phase III, double-blind, placebo-controlled trial (COVACTA) among hospitalized patients with severe coronavirus disease 2019 (COVID-19) pneumonia. We created a real-world external comparator arm mirroring the COVACTA trial to confirm findings and assess the feasibility of using an external comparator arm to supplement an RCT. Eligible COVACTA participants in both the tocilizumab treatment and placebo arms were matched 1:1 using propensity score matching to persons without tocilizumab exposure in an external comparator arm. Adjusted Cox proportional hazard models estimated differences in 28-day mortality comparing COVACTA participants to matched external comparator arm participants. Patients in the COVACTA tocilizumab treatment arm had a similar risk of death compared with patients in the external comparator arm (hazard ratio (HR): 1.09, 95% confidence interval (CI): 0.64-1.84) with similar estimated 28-day mortality in the COVACTA tocilizumab treatment arm compared with the external comparator arm (18%, 95% CI: 13-24 vs. 19%, 95% CI: 13-24, P > 0.9). COVACTA placebo treatment arm participants had a similar risk of mortality (adjusted HR: 0.69, 95% CI: 0.32-1.46) compared with the external comparator arm. Using an external comparator arm has the potential to supplement RCT data and support results of primary RCT analyses.

Risk Factors for Not Completing a 2-Dose Primary Series of Messenger RNA COVID-19 Vaccination in a Large Health Care System in Southern California: Retrospective Cohort Study

BACKGROUND

COVID-19 vaccination is crucial in combating the COVID-19 pandemic. Messenger RNA COVID-19 vaccines were initially authorized as a 2-dose primary series and have been widely used in the United States; completing the 2-dose primary series offers protection against infection, severe illness, and death. Understanding the risk factors for not completing the 2-dose primary series is critical to evaluate COVID-19 vaccination programs and promote completion of the 2-dose primary series.

OBJECTIVE

This study examined potential risk factors for not completing a 2-dose primary series of mRNA COVID-19 vaccination.

METHODS

We conducted a retrospective cohort study among members aged ≥18 years from a large integrated health care system, Kaiser Permanente Southern California, from December 14, 2020, to June 30, 2022. Noncompletion of the 2-dose primary series was defined as not completing the second dose within 6 months after receipt of the first dose. Crude noncompletion rates were estimated overall and by demographic characteristics, health care use patterns, comorbidity, and community-level socioeconomic factors. A Poisson regression model was fit to examine associations of individual-level and community-level risk factors with noncompletion of the 2-dose primary series.

RESULTS

Among 2.5 million recipients of ≥1 dose of mRNA COVID-19 vaccines, 3.3% (n=81,202) did not complete the second dose within 6 months. Members aged 25-44 years, 65-74 years, and ≥75 years were less likely to not complete the 2-dose primary series than those aged 18-24 years, while members aged 45-64 years were more likely to not complete the 2-dose primary series (adjusted risk ratio [aRR] 1.13, 95% CI 1.10-1.15). Male sex was associated with a higher risk of noncompletion (aRR 1.17, 95% CI 1.15-1.19). Hispanic and non-Hispanic Black race/ethnicity were associated with a lower risk of noncompletion (range aRR 0.78-0.91). Having Medicaid and prior influenza vaccination were associated with a higher risk of noncompletion. Having SARS-CoV-2 infection, experiencing an adverse event, or having an inpatient and emergency department visit during the minimum recommended dose intervals were associated with a higher risk of not completing the 2-dose primary series (aRR 1.98, 95% CI 1.85-2.12; 1.99, 95% CI 1.43-2.76; and 1.85, 95% CI 1.77-1.93, respectively). Those who received the first dose after June 30, 2021, were more likely to not complete the 2-dose primary series within 6 months of receipt of the first dose.

CONCLUSIONS

Despite limitations such as being a single-site study and the inability to consider social factors such as employment and vaccine attitudes, our study identified several risk factors for not completing a 2-dose primary series of mRNA vaccination, including being male; having Medicaid coverage; and experiencing SARS-CoV-2 infection, adverse events, or inpatient and emergency department visits during the minimum recommended dose intervals. These findings can inform future efforts in developing effective strategies to enhance vaccination coverage and improve the completion rate of necessary doses.

Increased vaccine sensitivity of an emerging SARS-CoV-2 variant

Host immune responses are a key source of selective pressure driving pathogen evolution. Emergence of many SARS-CoV-2 lineages has been associated with enhancements in their ability to evade population immunity resulting from both vaccination and infection. Here we show diverging trends of escape from vaccine-derived and infection-derived immunity for the emerging XBB/XBB.1.5 Omicron lineage. Among 31,739 patients tested in ambulatory settings in Southern California from December, 2022 to February, 2023, adjusted odds of prior receipt of 2, 3, 4, and ≥5 COVID-19 vaccine doses were 10% (95% confidence interval: 1-18%), 11% (3-19%), 13% (3-21%), and 25% (15-34%) lower, respectively, among cases infected with XBB/XBB.1.5 than among cases infected with other co-circulating lineages. Similarly, prior vaccination was associated with greater point estimates of protection against progression to hospitalization among cases with XBB/XBB.1.5 than among non-XBB/XBB.1.5 cases (70% [30-87%] and 48% [7-71%], respectively, for recipients of ≥4 doses). In contrast, cases infected with XBB/XBB.1.5 had 17% (11-24%) and 40% (19-65%) higher adjusted odds of having experienced 1 and ≥2 prior documented infections, respectively, including with pre-Omicron variants. As immunity acquired from SARS-CoV-2 infection becomes increasingly widespread, fitness costs associated with enhanced vaccine sensitivity in XBB/XBB.1.5 may be offset by increased ability to evade infection-derived host responses.

Impact of California's Senate Bill 27 on Antimicrobial-Resistant Escherichia coli Urinary Tract Infection in Humans: Protocol for a Study of Methods and Baseline Data

BACKGROUND

Overuse of antibiotics contributes to antimicrobial resistance (AMR) and is a growing threat to human health worldwide. Previous work suggests a link between antimicrobial use in poultry and human AMR extraintestinal pathogenic Escherichia coli (E coli) urinary tract infections (UTIs). However, few US-based studies exist, and none have comprehensively assessed both foodborne and environmental pathways using advanced molecular and spatial epidemiologic methods in a quasi-experimental design. Recently, California enacted Senate Bill 27 (SB27), which changed previous policy to require a veterinarian's prescription for the use of antibiotic drugs, and which banned antibiotic use for disease prevention in livestock. This provided an opportunity to evaluate whether SB27 will result in a reduction in antimicrobial-resistant infections in humans.

OBJECTIVE

We describe in detail the methods implemented to achieve the overarching objective of this study to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTIs.

METHODS

A summary of the overall approach and the partnerships between Columbia University, George Washington University (GWU), Johns Hopkins Bloomberg School of Public Health, Kaiser Permanente Southern California (KPSC) Research and Evaluation, the Natural Resources Defense Council, Sanger Institute at Stanford University, Sutter Health Center for Health Systems Research, the University of Cambridge, and the University of Oxford is presented. The collection, quality control testing, and shipment of retail meat and clinical samples are described. Retail meat (chicken, beef, turkey, and pork) was purchased from stores throughout Southern California from 2017 to 2021. After processing at KPSC, it was shipped to GWU for testing. From 2016 to 2021, after clinical specimens were processed for routine clinical purposes and immediately before discarding, those with isolated colonies of E coli, Campylobacter, and Salmonella from KPSC members were collected and processed to be shipped for testing at GWU. Detailed methods of the isolation and testing as well as the whole-genome sequencing of the meat and clinical samples at GWU are described. KPSC electronic health record data were used to track UTI cases and AMR patterns among the cultured specimens. Similarly, Sutter Health electronic health record data were used to track UTI cases in its Northern California patient population.

RESULTS

From 2017 to 2021, overall, 12,616 retail meat samples were purchased from 472 unique stores across Southern California. In addition, 31,643 positive clinical cultures were collected from KPSC members during the same study period.

CONCLUSIONS

Here, we presented data collection methods for the study, which was conducted to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTI. To date, it is one of the largest studies of its kind to be conducted. The data collected during this study will be used as the foundation for future analyses specific to the various objectives of this large body of work.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/45109.

Effectiveness of nirmatrelvir-ritonavir in preventing hospital admissions and deaths in people with COVID-19: a cohort study in a large US health-care system

BACKGROUND

In the USA, oral nirmatrelvir-ritonavir is authorised for use in patients aged 12 years or older with mild-to-moderate COVID-19 who are at risk of progression to severe disease and hospitalisation. We aimed to establish the effectiveness of nirmatrelvir-ritonavir in preventing hospital admissions and death in people with COVID-19 in an outpatient prescribing context in the USA.

METHODS

In this matched observational outpatient cohort study in the Kaiser Permanente Southern California (CA, USA) health-care system, data were extracted from electronic health records of non-hospitalised patients aged 12 years or older who received a positive SARS-CoV-2 PCR test result (their index test) between April 8 and Oct 7, 2022, and had not received another positive test result within the preceding 90 days. We compared outcomes between people who received nirmatrelvir-ritonavir and those who did not receive nirmatrelvir-ritonavir by matching cases by date, age, sex, clinical status (including care received, the presence or absence of acute COVID-19 symptoms at testing, and time from symptom onset to testing), vaccination history, comorbidities, health-care seeking during the previous year, and BMI. Our primary endpoint was the estimated effectiveness of nirmatrelvir-ritonavir in preventing hospital admissions or death within 30 days of a positive test for SARS-CoV-2.

FINDINGS

7274 nirmatrelvir-ritonavir recipients and 126 152 non-recipients with positive SARS-CoV-2 tests were included in our study. 5472 (75·2%) treatment recipients and 84 657 (67·1%) non-recipients were tested within 5 days of symptom onset. Nirmatrelvir-ritonavir had an overall estimated effectiveness of 53·6% (95% CI 6·6-77·0) in preventing hospital admission or death within 30 days of a positive test for SARS-CoV-2, which increased to 79·6% (33·9-93·8) when nirmatrelvir-ritonavir was dispensed within 5 days of symptom onset. Within the subgroup of patients tested within 5 days of symptom onset and whose treatment was dispensed on the day of their test, the estimated effectiveness of nirmatrelvir-ritonavir was 89·6% (50·2-97·8).

INTERPRETATION

In a setting with high levels of COVID-19 vaccine uptake, nirmatrelvir-ritonavir effectively reduced the risk of hospital admission or death within 30 days of a positive outpatient SARS-CoV-2 test.

FUNDING

US Centers for Disease Control and Prevention and US National Institutes of Health.

Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome

Expansion of the SARS-CoV-2 BA.4 and BA.5 Omicron subvariants in populations with prevalent immunity from prior infection and vaccination, and associated burden of severe COVID-19, has raised concerns about epidemiologic characteristics of these lineages including their association with immune escape or severe clinical outcomes. Here we show that BA.4/BA.5 cases in a large US healthcare system had at least 55% (95% confidence interval: 43-69%) higher adjusted odds of prior documented infection than time-matched BA.2 cases, as well as 15% (9-21%) and 38% (27-49%) higher adjusted odds of having received 3 and ≥4 COVID-19 vaccine doses, respectively. However, after adjusting for differences in epidemiologic characteristics among cases with each lineage, BA.4/BA.5 infection was not associated with differential risk of emergency department presentation, hospital admission, or intensive care unit admission following an initial outpatient diagnosis. This finding held in sensitivity analyses correcting for potential exposure misclassification resulting from unascertained prior infections. Our results demonstrate that the reduced severity associated with prior (BA.1 and BA.2) Omicron lineages, relative to the Delta variant, has persisted with BA.4/BA.5, despite the association of BA.4/BA.5 with increased risk of breakthrough infection among previously vaccinated or infected individuals.

Effectiveness and durability of BNT162b2 vaccine against hospital and emergency department admissions due to SARS-CoV-2 omicron sub-lineages BA.1 and BA.2 in a large health system in the USA: a test-negative, case-control study

BACKGROUND

The SARS-CoV-2 omicron (B.1.1.529 BA.1) lineage was first detected in November, 2021, and is associated with reduced vaccine effectiveness. By March, 2022, BA.1 had been replaced by sub-lineage BA.2 in the USA. As new variants evolve, vaccine performance must be continually assessed. We aimed to evaluate the effectiveness and durability of BNT162b2 (Pfizer-BioNTech) against hospital and emergency department admissions for BA.1 and BA.2.

METHODS

In this test-negative, case-control study, we sourced data from the electronic health records of adult (aged ≥18 years) members of Kaiser Permanente Southern California (KPSC), which is a health-care system in the USA, who were admitted to one of 15 KPSC hospitals or emergency departments (without subsequent hospitalisation) between Dec 27, 2021, and June 4, 2022, with an acute respiratory infection and were tested for SARS-CoV-2 by RT-PCR. Omicron sub-lineage was determined by use of sequencing, spike gene target failure, and the predominance of variants in certain time periods. Our main outcome was the effectiveness of two or three doses of BNT162b2 in preventing emergency department or hospital admission. Variant-specific vaccine effectiveness was evaluated by comparing the odds ratios from logistic regression models of vaccination between test-positive cases and test-negative controls, adjusting for the month of admission, age, sex, race and ethnicity, body-mass index, Charlson Comorbidity Index, previous influenza or pneumococcal vaccines, and previous SARS-CoV-2 infection. We also assessed effectiveness by the time since vaccination. This study is registered at ClinicalTrials.gov, NCT04848584, and is ongoing.

FINDINGS

Of 65 813 total admissions during the study period, we included 16 994 in our analyses, of which 7435 were due to BA.1, 1056 were due to BA.2, and 8503 were not due to SARS-CoV-2. In adjusted analyses, two-dose vaccine effectiveness was 40% (95% CI 27 to 50) for hospitalisation and 29% (18 to 38) for emergency department admission against BA.1 and 56% (31 to 72) for hospitalisation and 16% (-5 to 33) for emergency department admission against BA.2. Three-dose vaccine effectiveness was 79% (74 to 83) for hospitalisation and 72% (67 to 77) for emergency department admission against BA.1 and 71% (55 to 81) for hospitalisation and 21% (1 to 37) for emergency department admission against BA.2. Less than 3 months after the third dose, vaccine effectiveness was 80% (74 to 84) for hospitalisation and 74% (69 to 78) for emergency department admission against BA.1. Vaccine effectiveness 3 months or more after the third dose was 76% (69 to 82) against BA.1-related hospitalisation and 65% (56 to 73) against BA.1-related emergency department admission. Against BA.2, vaccine effectiveness was 74% (47 to 87) for hospitalisation and 59% (40 to 72) for emergency department admission at less than 3 months after the third dose and 70% (53 to 81) for hospitalisation and 5% (-21 to 25) for emergency department admission at 3 months or more after the third dose.

INTERPRETATION

Two doses of BNT162b2 provided only partial protection against BA.1-related and BA.2-related hospital and emergency department admission, which underscores the need for booster doses against omicron. Although three doses offered high levels of protection (≥70%) against hospitalisation, variant-adapted vaccines are probably needed to improve protection against less severe endpoints, like emergency department admission, especially for BA.2.

FUNDING

Pfizer.

BNT162b2 against COVID-19-associated Emergency Department and Urgent Care Visits among Children 5-11 Years of Age: a Test Negative Design

In a 1:1 matched test-negative design among 5-11-year-olds in the Kaiser Permanente Southern California health system (n=3984), BNT162b2 effectiveness against omicron-related emergency department or urgent care encounters was 60% [95%CI: 47-69] <3 months post-dose-two and 28% [8-43] after ≥3 months. A booster improved protection to 77% [53-88].

A safety study evaluating non-COVID-19 mortality risk following COVID-19 vaccination

BACKGROUND

The safety of COVID-19 vaccines plays an important role in addressing vaccine hesitancy. We conducted a large cohort study to evaluate the risk of non-COVID-19 mortality after COVID-19 vaccination while adjusting for confounders including individual-level demographics, clinical risk factors, health care utilization, and community-level socioeconomic risk factors.

METHODS

The retrospective cohort study consisted of members from seven Vaccine Safety Datalink sites from December 14, 2020 through August 31, 2021. We conducted three separate analyses for each of the three COVID-19 vaccines used in the US. Crude non-COVID-19 mortality rates were reported by vaccine type, age, sex, and race/ethnicity. The counting process model for survival analyses was used to analyze non-COVID-19 mortality where a new observation period began when the vaccination status changed upon receipt of the first dose and the second dose. We used calendar time as the basic time scale in survival analyses to implicitly adjust for season and other temporal trend factors. A propensity score approach was used to adjust for the potential imbalance in confounders between the vaccinated and comparison groups.

RESULTS

For each vaccine type and across age, sex, and race/ethnicity groups, crude non-COVID-19 mortality rates among COVID-19 vaccinees were lower than those among comparators. After adjusting for confounders with the propensity score approach, the adjusted hazard ratios (aHRs) were 0.46 (95% confidence interval [CI], 0.44-0.49) after dose 1 and 0.48 (95% CI, 0.46-0.50) after dose 2 of the BNT162b2 vaccine, 0.41 (95% CI, 0.39-0.44) after dose 1 and 0.38 (95% CI, 0.37-0.40) after dose 2 of the mRNA-1273 vaccine, and 0.55 (95% CI, 0.51-0.59) after receipt of Ad26.COV2.S.

CONCLUSION

While residual confounding bias remained after adjusting for several individual-level and community-level risk factors, no increased risk was found for non-COVID-19 mortality among recipients of three COVID-19 vaccines used in the US.

Effectiveness of nirmatrelvir-ritonavir against hospital admission or death: a cohort study in a large US healthcare system

BACKGROUND

In the United States, oral nirmatrelvir-ritonavir (PaxlovidTM) is authorized for use among patients aged 12+ years with mild-to-moderate SARS-CoV-2 infection who are at risk for progression to severe COVID-19, including hospitalization. However, effectiveness under current real-world prescribing practices in outpatient settings is unclear.

METHODS

We undertook a matched observational cohort study of non-hospitalized cases with SARS-CoV-2 infection to compare outcomes among those who received or did not receive nirmatrelvir-ritonavir within the Kaiser Permanente Southern California healthcare system. Cases were matched on testing date, age, sex, clinical status (including care received, presence or absence of acute COVID-19 symptoms at testing, and time from symptom onset to testing), history of vaccination, Charlson comorbidity index, prior-year healthcare utilization, and body mass index. Primary analyses evaluated effectiveness of nirmatrelvir-ritonavir in preventing hospital admission or death within 30 days after a positive test. Secondary analyses evaluated effectiveness against intensive care unit admission, mechanical ventilation, or death within 60 days after a positive test. We measured treatment effectiveness as (1-adjusted hazards ratio [aHR])*100%, estimating the aHR via Cox proportional hazards models.

RESULTS

Analyses included 7,274 nirmatrelvir-ritonavir recipients and 126,152 non-recipients with positive results from SARS-CoV-2 tests undertaken in outpatient settings between 8 April and 7 October, 2022. Overall, 114,208 (85.6%) and 81,739 (61.3%) of 133,426 participants had received 2+ and 3+ COVID-19 vaccine doses, respectively. A total of 111,489 (83.6% of 133,426) cases were symptomatic at the point of testing, with 5,472 (75.2% of 7,274) treatment recipients and 84,657 (67.1% of 126,152) non-recipients testing within 0-5 days after symptom onset. Effectiveness in preventing hospital admission or death within 30 days after a positive test was 79.6% (95% confidence interval: 33.9% to 93.8%) for cases dispensed nirmatrelvir-ritonavir within 0-5 days after symptom onset; within the subgroup of cases tested 0-5 days after symptom onset and dispensed treatment on the day of their test, effectiveness was 89.6% (50.2% to 97.8%). Effectiveness declined to 43.8% (-33.3% to 81.7%) for treatment course dispensed 6+ days after symptom onset or to cases who were not experiencing acute clinical symptoms. Overall, for cases dispensed treatment at any time within their clinical course, effectiveness was 53.6% (6.6% to 77.0%). Effectiveness in preventing the secondary endpoint of intensive care unit admission, mechanical ventilation, or death within 60 days after a positive test was 89.2% (-25.0% to 99.3%) for cases dispensed treatment 0-5 days after symptom onset and 84.1% (18.8% to 96.9%) for cases dispensed treatment at any time. Subgroup analyses identified similar effectiveness estimates among cases who had received 2+ or 3+ COVID-19 vaccine doses.

IMPLICATIONS

In a setting with high levels of COVID-19 vaccine and booster uptake, receipt of nirmatrelvir-ritonavir 0-5 days after symptom onset was associated with substantial reductions in risk of hospital admission or death within 30 days after a positive outpatient SARS-CoV-2 test.

Analysis of mRNA COVID-19 Vaccine Uptake Among Immunocompromised Individuals in a Large US Health System

Importance

Immunocompromised individuals are at increased risk for severe outcomes due to SARS-CoV-2 infection. Given the varying and complex nature of COVID-19 vaccination recommendations, it is important to understand COVID-19 vaccine uptake in this vulnerable population.

Objective

To assess mRNA COVID-19 vaccine uptake and factors associated with uptake among immunocompromised individuals from December 14, 2020, through August 6, 2022.

Design, Setting, and Participants

This cohort study was conducted with patients of Kaiser Permanente Southern California (KPSC), an integrated health care system in the US. The study included patients aged 18 years or older who were immunocompromised (individuals with an immunocompromising condition or patients who received immunosuppressive medications in the year prior to December 14, 2020) and still met criteria for being immunocompromised 1 year later.

Exposures

Age, sex, self-identified race and ethnicity, prior positive COVID-19 test result, immunocompromising condition, immunomodulating medication, comorbidities, health care utilization, and neighborhood median income.

Main Outcomes and Measures

Outcomes were the number of doses of mRNA COVID-19 vaccine received and the factors associated with receipt of at least 4 doses, estimated by hazard ratios (HRs) and 95% Wald CIs via Cox proportional hazards regression. Statistical analyses were conducted between August 9 and 23, 2022.

Results

Overall, 42 697 immunocompromised individuals met the study eligibility criteria. Among these, 18 789 (44.0%) were aged 65 years or older; 20 061 (47.0%) were women and 22 635 (53.0%) were men. With regard to race and ethnicity, 4295 participants (10.1%) identified as Asian or Pacific Islander, 5174 (12.1%) as Black, 14 289 (33.5%) as Hispanic, and 17 902 (41.9%) as White. As of the end of the study period and after accounting for participant censoring due to death or disenrollment from the KPSC health plan, 78.0% of immunocompromised individuals had received a third dose of mRNA COVID-19 vaccine. Only 41.0% had received a fourth dose, which corresponds to a primary series and a monovalent booster dose for immunocompromised individuals. Uptake of a fifth dose was only 0.9% following the US Centers for Disease Control and Prevention (CDC) recommendation to receive a second monovalent booster (ie, fifth dose). Adults aged 65 years or older (HR, 3.95 [95% CI, 3.70-4.22]) were more likely to receive at least 4 doses compared with those aged 18 to 44 years or 45 to 64 years (2.52 [2.36-2.69]). Hispanic and non-Hispanic Black adults (HR, 0.77 [95% CI, 0.74-0.80] and 0.82 [0.78-0.87], respectively, compared with non-Hispanic White adults), individuals with prior documented SARS-CoV-2 infection (0.71 [0.62-0.81] compared with those without), and individuals receiving high-dose corticosteroids (0.88 [0.81-0.95] compared with those who were not) were less likely to receive at least 4 doses.

Conclusions and Relevance

These findings suggest that adherence to CDC mRNA monovalent COVID-19 booster dose recommendations among immunocompromised individuals was low. Given the increased risk for severe COVID-19 in this vulnerable population and the well-established additional protection afforded by booster doses, targeted and tailored efforts to ensure that immunocompromised individuals remain up to date with COVID-19 booster dose recommendations are warranted.

Natural Language Processing for Improved Characterization of COVID-19 Symptoms: Observational Study of 350,000 Patients in a Large Integrated Health Care System

BACKGROUND

Natural language processing (NLP) of unstructured text from electronic medical records (EMR) can improve the characterization of COVID-19 signs and symptoms, but large-scale studies demonstrating the real-world application and validation of NLP for this purpose are limited.

OBJECTIVE

The aim of this paper is to assess the contribution of NLP when identifying COVID-19 signs and symptoms from EMR.

METHODS

This study was conducted in Kaiser Permanente Southern California, a large integrated health care system using data from all patients with positive SARS-CoV-2 laboratory tests from March 2020 to May 2021. An NLP algorithm was developed to extract free text from EMR on 12 established signs and symptoms of COVID-19, including fever, cough, headache, fatigue, dyspnea, chills, sore throat, myalgia, anosmia, diarrhea, vomiting or nausea, and abdominal pain. The proportion of patients reporting each symptom and the corresponding onset dates were described before and after supplementing structured EMR data with NLP-extracted signs and symptoms. A random sample of 100 chart-reviewed and adjudicated SARS-CoV-2-positive cases were used to validate the algorithm performance.

RESULTS

A total of 359,938 patients (mean age 40.4 [SD 19.2] years; 191,630/359,938, 53% female) with confirmed SARS-CoV-2 infection were identified over the study period. The most common signs and symptoms identified through NLP-supplemented analyses were cough (220,631/359,938, 61%), fever (185,618/359,938, 52%), myalgia (153,042/359,938, 43%), and headache (144,705/359,938, 40%). The NLP algorithm identified an additional 55,568 (15%) symptomatic cases that were previously defined as asymptomatic using structured data alone. The proportion of additional cases with each selected symptom identified in NLP-supplemented analysis varied across the selected symptoms, from 29% (63,742/220,631) of all records for cough to 64% (38,884/60,865) of all records with nausea or vomiting. Of the 295,305 symptomatic patients, the median time from symptom onset to testing was 3 days using structured data alone, whereas the NLP algorithm identified signs or symptoms approximately 1 day earlier. When validated against chart-reviewed cases, the NLP algorithm successfully identified signs and symptoms with consistently high sensitivity (ranging from 87% to 100%) and specificity (94% to 100%).

CONCLUSIONS

These findings demonstrate that NLP can identify and characterize a broad set of COVID-19 signs and symptoms from unstructured EMR data with enhanced detail and timeliness compared with structured data alone.

Retrospective cohort study to assess the association between treatment with tocilizumab and mortality among mechanically ventilated patients with COVID-19

OBJECTIVES

Assess the association between tocilizumab administration and clinical outcomes among mechanically ventilated patients with COVID-19 pneumonia.

DESIGN

Retrospective cohort study.

SETTING

Large integrated health system with 9 million members in California, USA.

PARTICIPANTS

4185 Kaiser Permanente members hospitalised with COVID-19 pneumonia requiring invasive mechanical ventilation (IMV).

INTERVENTIONS

Receipt of tocilizumab within 10 days of initiation of IMV.

OUTCOME MEASURES

Using a retrospective cohort of consecutive patients hospitalised with COVID-19 pneumonia who required IMV in a large integrated health system in California, USA, we assessed the association between tocilizumab administration and 28-day mortality, time to extubation from IMV and time to hospital discharge.

RESULTS

Among 4185 patients, 184 received tocilizumab and 4001 patients did not receive tocilizumab within 10 days of initiation of IMV. After inverse probability weighting, baseline characteristics were well balanced between groups. Patients treated with tocilizumab had a similar risk of death in the 28 days after intubation compared with patients not treated with tocilizumab (adjusted HR (aHR), 1.21, 95% CI 0.98 to 1.50), but did have a significantly longer time-to-extubation (aHR 0.71; 95% CI 0.57 to 0.88) and time-to-hospital-discharge (aHR 0.66; 95% CI 0.50 to 0.88). However, patients treated with tocilizumab ≤2 days after initiation of IMV had a similar risk of mortality (aHR 1.47; 95% CI 0.96 to 2.26), but significantly shorter time-to-extubation (aHR 0.37; 95% CI 0.23 to 0.58) and time-to-hospital-discharge (aHR 0.31; 95% CI CI 0.17 to 0.56) compared with patients treated with tocilizumab 3-10 days after initiation of IMV.

CONCLUSIONS

Among mechanically ventilated patients with COVID-19, the risk of death in the 28-day follow-up period was similar, but time-to-extubation and time-to-hospital-discharge were longer in patients who received tocilizumab within 10 days of initiation of IMV compared with patients who did not receive tocilizumab.

Effectiveness Associated With BNT162b2 Vaccine Against Emergency Department and Urgent Care Encounters for Delta and Omicron SARS-CoV-2 Infection Among Adolescents Aged 12 to 17 Years

Importance

Data about the duration of protection of 2 and 3 doses of BNT162b2 in children and adolescents are needed to help inform recommendations for boosters in this age group.

Objective

To evaluate vaccine effectiveness (VE) and durability associated with 2 doses of BNT162b2 against Delta- and Omicron-related emergency department (ED) and urgent care (UC) encounters among adolescents aged 12 to 17 years and to estimate VE associated with 3 doses against these same outcomes.

Design, Setting, and Participants

This test-negative case-control study was conducted at Kaiser Permanente Southern California, an integrated health care system using electronic health records in the US. Participants included Kaiser Permanente Southern California members ages 12 to 17 years with an ED or UC encounter from November 1, 2021, through March 18, 2022, for acute respiratory infection who were tested for SARS-CoV-2 via a reverse transction-polymerase chain reaction test. Analyses were conducted from March 21 to June 22, 2022.

Exposures

BNT162b2 vaccination status ascertained from electronic health records and state registry data.

Main Outcomes and Measures

The main outcome was VE associated with BNT162b2 against ED and UC encounters related to Delta or Omicron variant SARS-CoV-2 infection.

Results

Analyses were conducted among 3168 adolescents, including 1004 with ED visits and 2164 with UC visits. Median (IQR) age was 15 (13-16) years, and 1461 (46.1%) were boys. In adjusted analyses, VE associated with 2 doses of BNT162b2 against ED or UC encounters was highest within the first 2 months for both Delta (89% [95% CI, 69% to 96%]) and Omicron (73% [95% CI, 54% to 84%]) variants but waned to 49% (95% CI, 27% to 65%) for the Delta variant and 16% (95% CI, -7% to 34%) for the Omicron variant at 6 months and beyond. A third dose of BNT162b2 was associated with improved protection against the Omicron variant (87% [95% CI, 72% to 94%]) after a median (IQR) of 19 (9-32) days after dose 3.

Conclusions and Relevance

These findings suggest that 2 doses of the BNT162b2 COVID-19 vaccine were associated with high levels of protection against ED and UC encounters related to the Delta and Omicron variants of SARS-CoV-2 in the first few months after vaccination. However, effectiveness waned over time, especially against Omicron. A third dose of BNT162b2 was associated with improved protection against Omicron beyond that seen initially after 2 doses, underscoring the importance of boosters for adolescents aged 12 to 17 years.

Durability of BNT162b2 vaccine against hospital and emergency department admissions due to the omicron and delta variants in a large health system in the USA: a test-negative case-control study

BACKGROUND

The duration of protection against the omicron (B.1.1.529) variant for current COVID-19 vaccines is not well characterised. Vaccine-specific estimates are especially needed. We aimed to evaluate the effectiveness and durability of two and three doses of the BNT162b2 (Pfizer-BioNTech) mRNA vaccine against hospital and emergency department admissions due to the delta (B.1.617.2) and omicron variants.

METHODS

In this case-control study with a test-negative design, we analysed electronic health records of members of Kaiser Permanente Southern California (KPSC), a large integrated health system in California, USA, from Dec 1, 2021, to Feb 6, 2022. Vaccine effectiveness was calculated in KPSC patients aged 18 years and older admitted to hospital or an emergency department (without a subsequent hospital admission) with a diagnosis of acute respiratory infection and tested for SARS-CoV-2 via PCR. Adjusted vaccine effectiveness was estimated with odds ratios from adjusted logistic regression models. This study is registered with ClinicalTrials.gov (NCT04848584).

FINDINGS

Analyses were done for 11 123 hospital or emergency department admissions. In adjusted analyses, effectiveness of two doses of the BNT162b2 vaccine against the omicron variant was 41% (95% CI 21-55) against hospital admission and 31% (16-43) against emergency department admission at 9 months or longer after the second dose. After three doses, effectiveness of BNT162b2 against hospital admission due to the omicron variant was 85% (95% CI 80-89) at less than 3 months but fell to 55% (28-71) at 3 months or longer, although confidence intervals were wide for the latter estimate. Against emergency department admission, the effectiveness of three doses of BNT162b2 against the omicron variant was 77% (72-81) at less than 3 months but fell to 53% (36-66) at 3 months or longer. Trends in waning against SARS-CoV-2 outcomes due to the delta variant were generally similar, but with higher effectiveness estimates at each timepoint than those seen for the omicron variant.

INTERPRETATION

Three doses of BNT162b2 conferred high protection against hospital and emergency department admission due to both the delta and omicron variants in the first 3 months after vaccination. However, 3 months after receipt of a third dose, waning was apparent against SARS-CoV-2 outcomes due to the omicron variant, including hospital admission. Additional doses of current, adapted, or novel COVD-19 vaccines might be needed to maintain high levels of protection against subsequent waves of SARS-CoV-2 caused by the omicron variant or future variants with similar escape potential.

FUNDING

Pfizer.

Hospitalization and Emergency Department Encounters for COVID-19 After Paxlovid Treatment - California, December 2021-May 2022

Nirmatrelvir/ritonavir (Paxlovid) is a combination protease inhibitor that blocks replication of SARS-CoV-2 (the virus that causes COVID-19) and has been shown to reduce the risk for hospitalization and death among patients with mild to moderate COVID-19 who are at risk for progression to severe disease* (1). In December 2021, the Food and Drug Administration (FDA) issued an Emergency Use Authorization (EUA) for early treatment with Paxlovid among persons with mild to moderate cases of COVID-19 who are at high risk for progression to severe disease (2). FDA and a small number of published case reports have documented recurrence of COVID-19 symptoms or a positive viral test result (COVID-19 rebound) 2-8 days after recovery or a negative SARS-CoV-2 test result among patients treated with Paxlovid (3-7); however, large-scale studies investigating severe illness after Paxlovid treatment are limited. This study used electronic health record (EHR) data from a large integrated health care system in California (Kaiser Permanente Southern California [KPSC]) to describe hospital admissions and emergency department (ED) encounters related to SARS-CoV-2 infections during the 5-15 days after pharmacy dispensation of a 5-day treatment course of Paxlovid. Among 5,287 persons aged ≥12 years who received Paxlovid during December 31, 2021-May 26, 2022, 73% had received ≥3 doses of COVID-19 vaccine^†, and 8% were unvaccinated. During the 5-15 days after Paxlovid treatment was dispensed, six hospitalizations and 39 ED encounters considered to be related to SARS-CoV-2 infection were identified, representing <1% of all patients to whom Paxlovid treatment was dispensed during the study period. Among these 45 persons, 21 (47%) were aged ≥65 years, and 35 (78%) had at least one underlying medical condition^§ (8). This study found that hospitalization or ED encounters for COVID-19 during the 5-15 days after Paxlovid treatment was dispensed for mild to moderate COVID-19 illness were rarely identified. When administered as an early-stage treatment, Paxlovid might prevent COVID-19-related hospitalization among persons with mild to moderate cases of COVID-19 who are at risk for progression to severe disease.

Changes in incidence rates of outcomes of interest in vaccine safety studies during the COVID-19 pandemic

BACKGROUND

The COVID-19 pandemic caused an abrupt drop in in-person health care (inpatient, Emergency Department, outpatient) and an increase in telehealth care, which poses challenges in vaccine safety studies that identify outcomes from in-person encounters. We examined the changes in incidence rates of selected encounter-based outcomes during the COVID-19 pandemic.

METHODS

We assembled a cohort of members from 8 Vaccine Safety Datalink sites from January 1, 2017 through December 31, 2020. Using ICD-10 diagnosis codes or laboratory criteria, we identified 21 incident outcomes in traditional in-person settings and all settings. We defined 4 periods in 2020: January-February (pre-pandemic), April-June (early pandemic), July-September (middle pandemic), and October-December (late pandemic). We defined four corresponding periods in each year during 2017-2019. We calculated incidence rates, conducted difference in difference (DiD) analyses, and reported ratios of incidence rate ratios (RRR) to examine changes in rates from pre-pandemic to early, middle, and late pandemic in 2020, after adjusting for changes across similar periods in 2017-2019.

RESULTS

Among > 10 million members, regardless of setting and after adjusting for changes during 2017-2019, we found that incidence rates of acute disseminated encephalomyelitis, encephalitis/myelitis/encephalomyelitis/meningoencephalitis, and thrombotic thrombocytopenic purpura did not significantly change from the pre-pandemic to early, middle or late pandemic periods (p-values ≥ 0.05). Incidence rates decreased from the pre-pandemic to early pandemic period during 2020 for acute myocardial infarction, anaphylaxis, appendicitis, Bell's palsy, convulsions/seizures, Guillain-Barré syndrome, immune thrombocytopenia (ITP), narcolepsy/cataplexy, hemorrhagic stroke, ischemic stroke, and venous thromboembolism (p-values < 0.05). Incidence rates of Bell's palsy, ITP, and narcolepsy/cataplexy were higher in all settings than in traditional in-person settings during the three pandemic periods (p-values < 0.05).

CONCLUSION

Rates of some clinical outcomes during the pandemic changed and should not be used as historical background rates in vaccine safety studies. Inclusion of telehealth visits should be considered for vaccine studies involving Bell's palsy, ITP, and narcolepsy/cataplexy.

Effectiveness of a third dose of BNT162b2 mRNA COVID-19 vaccine in a large US health system: A retrospective cohort study

Background

Globally, recommendations are expanding for third (booster) doses of BNT162b2 (Pfizer-BioNTech). In the United States, as of November 19, 2021, boosters were recommended for all adults aged 18 years and older. We evaluated the effectiveness of a third dose of BNT162b2 among adults in a large US integrated health system.

Methods

In this retrospective cohort study, we analyzed electronic health records from Kaiser Permanente Southern California between Dec 14, 2020 and Dec 5, 2021 to assess vaccine effectiveness (VE) of two and three doses of BNT162b2 against SARS-CoV-2 infections (without hospital admission) andCOVID-19-related hospital admission. VE was calculated using hazards ratios from adjusted Cox models.

Findings

After only two doses, VE against infection declined from 85% (95% CI 83-86) during the first month to 49% (46-51) ≥ 7 months following vaccination. Overall VE against hospitalization was 90% (95% CI 86-92) within one month and did not wane, however, effectiveness against hospitalization appeared to wane among immunocompromised individuals but was not statistically significant (93% [72-98] at 1 month to 74% [45-88] after ≥ 7 months; p=0·490). Three-dose VE (median follow-up 1·3 months [SD 0·6]) was 88% (95% CI 86-89) against infection and 97% (95-98) against hospitalization. Effectiveness after three doses was higher than that seen one month after receiving only two doses for both outcomes. Relative VE of three doses compared to two (with at least six months after the second dose) was 75% (95% CI 71-78) against infections and 70% (48-83) against hospital admissions.

Interpretation

These data support the benefit of broad BNT162b2 booster recommendations, as three doses confers comparable, if not better, protection against SARS-CoV-2 infections and hospital admission as was seen soon after receiving two doses.

Funding

Pfizer Inc.

906. Characteristics of Chronic Hepatitis B Patients with Severe Outcomes in a Large Integrated Healthcare System - 2008-2019

Background

It is estimated that there are 1.59 million cases of chronic hepatitis B virus (HBV) infection (CHB) in the United States. HBV infection is highest among men and non-Hispanic Asian adults. CHB can lead to liver damage, cirrhosis, hepatocellular carcinoma, or death. However, the population that is most likely to develop severe outcomes is not as well-defined.

Methods

We evaluated electronic health record data from Kaiser Permanente Southern California adult members from 2008-2019 with at least 1 year of continuous membership, and with 2 successive, positive HBV lab results (HBV DNA, or HBsAg, or HBeAg) at least 6 months apart (indicative of CHB). Severe outcomes included incident hepatic decompensation, hepatocellular carcinoma (HCC), liver transplant and death, and prevalent and incident liver cirrhosis. For each outcome, we estimated the distribution of characteristics including age, sex, race/ethnicity, and lab values (alanine aminotransferase [ALT], alpha-fetoprotein [AFP], MELD score).

Results

Our final study population included 5,427 CHB-diagnosed patients with 411 (7.6%) cases of liver cirrhosis, 123 (2.3%) of hepatic decompensation, 65 (1.2%) of HCC, 8 (0.1%) of liver transplant, and 164 (3.0%) deaths. Compared to the total cohort, those who developed severe outcomes were older (median age for each outcome >50 years vs. 47 years in total CHB population). Among those with severe outcomes, the majority were male ( >56%) and Asian. Diabetes was more prevalent in patients with hepatic decompensation, HCC, and death versus the entire cohort (25% vs. 8%, respectively, P< 0.0001), and twice as prevalent among those with cirrhosis. All severe outcomes were associated with >2 x upper limit of normal ALT levels.

Conclusion

The characteristics of those with severe outcomes were consistent with those of overall CHB, although there was a 2-3 times higher prevalence of diabetes in those with severe outcomes. Identifying characteristics that are more prevalent in those with severe outcomes can help inform screening and management of CHB.

Disclosures

Ana Florea, PhD MPH, Gilead Inc. (Grant/Research Support) Prabhu Gounder, MD, Gilead Inc. (Grant/Research Support) Amandeep Sahota, MD, MS, Gilead Inc (Grant/Research Support) Katherine J. Pak, MS, Gilead (Grant/Research Support) Vennis Hong, MPH, Gilead Inc. (Research Grant or Support) Theresa M. Im, MPH, Gilead Inc. (Grant/Research Support) Sara Tartof, PhD, Gilead (Grant/Research Support, Scientific Research Study Investigator)

Effectiveness of mRNA BNT162b2 COVID-19 vaccine up to 6 months in a large integrated health system in the USA: a retrospective cohort study

BACKGROUND

Vaccine effectiveness studies have not differentiated the effect of the delta (B.1.617.2) variant and potential waning immunity in observed reductions in effectiveness against SARS-CoV-2 infections. We aimed to evaluate overall and variant-specific effectiveness of BNT162b2 (tozinameran, Pfizer-BioNTech) against SARS-CoV-2 infections and COVID-19-related hospital admissions by time since vaccination among members of a large US health-care system.

METHODS

In this retrospective cohort study, we analysed electronic health records of individuals (≥12 years) who were members of the health-care organisation Kaiser Permanente Southern California (CA, USA), to assess BNT162b2 vaccine effectiveness against SARS-CoV-2 infections and COVID-19-related hospital admissions for up to 6 months. Participants were required to have 1 year or more previous membership of the organisation. Outcomes comprised SARS-CoV-2 PCR-positive tests and COVID-19-related hospital admissions. Effectiveness calculations were based on hazard ratios from adjusted Cox models. This study was registered with ClinicalTrials.gov, NCT04848584.

FINDINGS

Between Dec 14, 2020, and Aug 8, 2021, of 4 920 549 individuals assessed for eligibility, we included 3 436 957 (median age 45 years [IQR 29-61]; 1 799 395 [52·4%] female and 1 637 394 [47·6%] male). For fully vaccinated individuals, effectiveness against SARS-CoV-2 infections was 73% (95% CI 72-74) and against COVID-19-related hospital admissions was 90% (89-92). Effectiveness against infections declined from 88% (95% CI 86-89) during the first month after full vaccination to 47% (43-51) after 5 months. Among sequenced infections, vaccine effectiveness against infections of the delta variant was high during the first month after full vaccination (93% [95% CI 85-97]) but declined to 53% [39-65] after 4 months. Effectiveness against other (non-delta) variants the first month after full vaccination was also high at 97% (95% CI 95-99), but waned to 67% (45-80) at 4-5 months. Vaccine effectiveness against hospital admissions for infections with the delta variant for all ages was high overall (93% [95% CI 84-96]) up to 6 months.

INTERPRETATION

Our results provide support for high effectiveness of BNT162b2 against hospital admissions up until around 6 months after being fully vaccinated, even in the face of widespread dissemination of the delta variant. Reduction in vaccine effectiveness against SARS-CoV-2 infections over time is probably primarily due to waning immunity with time rather than the delta variant escaping vaccine protection.

FUNDING

Pfizer.

Disparities in Outpatient and Telehealth Visits During the COVID-19 Pandemic in a Large Integrated Health Care Organization: Retrospective Cohort Study

Background

Dramatic decreases in outpatient visits and sudden increases in telehealth visits were observed during the COVID-19 pandemic, but it was unclear whether these changes differed by patient demographics and socioeconomic status.

Objective

This study aimed to assess the impact of the pandemic on in-person outpatient and telehealth visits (telephone and video) by demographic characteristics and household income in a diverse population.

Methods

We calculated weekly rates of outpatient and telehealth visits by age, sex, race/ethnicity, and neighborhood-level median household income among members of Kaiser Permanente Southern California (KPSC) from January 5, 2020, to October 31, 2020, and the corresponding period in 2019. We estimated the percentage change in visit rates during the early pandemic period (March 22 to April 25, 2020) and the late pandemic period (October 4 to October 31, 2020) from the prepandemic period (January 5 to March 7, 2020) in Poisson regression models for each subgroup while adjusting for seasonality using 2019 data. We examined if the changes in visit rates differed by subgroups statistically by comparing their 95% CIs.

Results

Among 4.56 million KPSC members enrolled in January 2020, 15.0% (n=682,947) were ≥65 years old, 51.5% (n=2,345,020) were female, 39.4% (n=1,795,994) were Hispanic, and 7.7% (n=350,721) lived in an area of median household income <US $40,000. Increases in telehealth visits during the pandemic varied across subgroups, while decreases in outpatient visits were similar, except by age. Among age groups, the ≥65 years population had the least increase in telehealth visits (236.6%, 95% CI 228.8%-244.5%), with 4.9 per one person-year during the early pandemic period versus 1.5 per one person-year during the prepandemic period. During the same periods, across racial/ethnic groups, Hispanic individuals had the largest increase in telehealth visits (295.5%, 95% CI 275.5%-316.5%). Across income levels, telehealth visits in the low-income group increased the most (313.5%, 95% CI 294.8%-333.1%). The rate of combined outpatient and telehealth visits in the Hispanic, non-Hispanic Black, and low-income groups returned to prepandemic levels by October 2020.

Conclusions

The Hispanic group and low-income group had the largest percentage increase in telehealth utilization in response to the COVID-19 pandemic. The use of virtual care potentially mitigated the impact of the pandemic on health care utilization in these vulnerable populations.

Sociodemographic Inequalities in Urinary Tract Infection in 2 Large California Health Systems

Background

Urinary tract infection (UTI) accounts for a substantial portion of outpatient visits and antibiotic prescriptions in the United States. Few studies have considered sociodemographic factors including low socioeconomic status (SES)—which may increase residential crowding, inappropriate antibiotic prescribing, or comorbidities—as UTI or multidrug-resistant (MDR) UTI risk factors.

Methods

We used 2015–2017 electronic health record data from 2 California health care systems to assess whether 3 sociodemographic factors—use of Medicaid, use of an interpreter, and census tract–level deprivation—were associated with overall UTI or MDR UTI. UTIs resistant to ≥3 antibiotic classes were considered MDR.

Results

Analyses included 601 352 UTI cases, 1 303 455 controls, and 424 977 urinary Escherichia coli isolates from Kaiser Permanente Southern California (KPSC) and Sutter Health in Northern California. The MDR prevalence was 10.4% at KPSC and 12.8% at Sutter Health. All 3 sociodemographic factors (ie, use of Medicaid, using an interpreter, and community deprivation) were associated increased risk of MDR UTI. For example, using an interpreter was associated with a 36% (relative risk [RR], 1.36; 95% CI, 1.31 to 1.40) and 28% (RR, 1.28; 95% CI, 1.22 to 1.34) increased risk of MDR UTI at KPSC and Sutter Health, respectively, adjusted for SES and other potential confounding variables. The 3 sociodemographic factors were only weakly associated with UTI overall.

Conclusions

We found low SES and use of an interpreter to be novel risk factors for MDR UTI in the United States.

Correction: Impact of the COVID-19 Pandemic on Health Care Utilization in a Large Integrated Health Care System: Retrospective Cohort Study

[This corrects the article DOI: 10.2196/26558.].

Impact of the COVID-19 Pandemic on Health Care Utilization in a Large Integrated Health Care System: Retrospective Cohort Study

Background

The COVID-19 pandemic has caused an abrupt reduction in the use of in-person health care, accompanied by a corresponding surge in the use of telehealth services. However, the extent and nature of changes in health care utilization during the pandemic may differ by care setting. Knowledge of the impact of the pandemic on health care utilization is important to health care organizations and policy makers.

Objective

The aims of this study are (1) to evaluate changes in in-person health care utilization and telehealth visits during the COVID-19 pandemic and (2) to assess the difference in changes in health care utilization between the pandemic year 2020 and the prepandemic year 2019.

Methods

We retrospectively assembled a cohort consisting of members of a large integrated health care organization, who were enrolled between January 6 and November 2, 2019 (prepandemic year), and between January 5 and October 31, 2020 (pandemic year). The rates of visits were calculated weekly for four settings: inpatient, emergency department (ED), outpatient, and telehealth. Using Poisson models, we assessed the impact of the pandemic on health care utilization during the early days of the pandemic and conducted difference-in-deference (DID) analyses to measure the changes in health care utilization, adjusting for the trend of health care utilization in the prepandemic year.

Results

In the early days of the pandemic, we observed significant reductions in inpatient, ED, and outpatient utilization (by 30.2%, 37.0%, and 80.9%, respectively). By contrast, there was a 4-fold increase in telehealth visits between weeks 8 (February 23) and 12 (March 22) in 2020. DID analyses revealed that after adjusting for prepandemic secular trends, the reductions in inpatient, ED, and outpatient visit rates in the early days of the pandemic were 1.6, 8.9, and 367.2 visits per 100 person-years (P<.001), respectively, while the increase in telehealth visits was 272.9 visits per 100 person-years (P<.001). Further analyses suggested that the increase in telehealth visits offset the reduction in outpatient visits by week 26 (June 28, 2020).

Conclusions

In-person health care utilization decreased drastically during the early period of the pandemic, but there was a corresponding increase in telehealth visits during the same period. By end-June 2020, the combined outpatient and telehealth visits had recovered to prepandemic levels.

Socio-demographic determinants of motorcycle speeding in Maha Sarakham, Thailand

Thailand has the highest road traffic fatality rate in Southeast Asia, making road safety a critical public health concern. A 2015 World Health Organization (WHO) Report showed that speeding behavior was the most important determinant for road traffic crashes in Thailand. Here, we aimed to examine associations of socio-demographic factors (gender, age, socioeconomic status) with self-reported motorcycle speeding behavior. Additionally, we examined a potential role of time discounting and risk preference as mediators in the association of socio-demographic factors with speeding. We used data obtained from the Mahasarakham University Social Network Survey 2018 (MSUSSS) (N = 150). We ran linear network autocorrelation models (lnam) to account for the data's social network structure. We found that males are more likely than females to engage in speeding behavior (β = 0.140, p = 0.001) and to discount the future (β = 5.175, p = 0.017). However, further causal mediation analysis showed that time discounting does not mediate the gender-speeding association (p for mediation = 0.540). Although socioeconomic status (subjective social class) was not associated with speeding (β = 0.039, p = 0.177), age was marginally associated with speeding (β = 0.005, p = 0.093). Future studies may consider using a larger sample.

Obesity and Mortality Among Patients Diagnosed With COVID-19: Results From an Integrated Health Care Organization

BACKGROUND

Obesity, race/ethnicity, and other correlated characteristics have emerged as high-profile risk factors for adverse coronavirus disease 2019 (COVID-19)-associated outcomes, yet studies have not adequately disentangled their effects.

OBJECTIVE

To determine the adjusted effect of body mass index (BMI), associated comorbidities, time, neighborhood-level sociodemographic factors, and other factors on risk for death due to COVID-19.

DESIGN

Retrospective cohort study.

SETTING

Kaiser Permanente Southern California, a large integrated health care organization.

PATIENTS

Kaiser Permanente Southern California members diagnosed with COVID-19 from 13 February to 2 May 2020.

MEASUREMENTS

Multivariable Poisson regression estimated the adjusted effect of BMI and other factors on risk for death at 21 days; models were also stratified by age and sex.

RESULTS

Among 6916 patients with COVID-19, there was a J-shaped association between BMI and risk for death, even after adjustment for obesity-related comorbidities. Compared with patients with a BMI of 18.5 to 24 kg/m², those with BMIs of 40 to 44 kg/m² and greater than 45 kg/m² had relative risks of 2.68 (95% CI, 1.43 to 5.04) and 4.18 (CI, 2.12 to 8.26), respectively. This risk was most striking among those aged 60 years or younger and men. Increased risk for death associated with Black or Latino race/ethnicity or other sociodemographic characteristics was not detected.

LIMITATION

Deaths occurring outside a health care setting and not captured in membership files may have been missed.

CONCLUSION

Obesity plays a profound role in risk for death from COVID-19, particularly in male patients and younger populations. Our capitated system with more equalized health care access may explain the absence of effect of racial/ethnic and socioeconomic disparities on death. Our data highlight the leading role of severe obesity over correlated risk factors, providing a target for early intervention.

PRIMARY FUNDING SOURCE

Roche-Genentech.

Differences in Estimates of Post-Herpetic Neuralgia Between Medical Chart Review and Self-Report

PURPOSE

Post-herpetic neuralgia (PHN) is a common herpes zoster (HZ) complication, where pain persists 90 days after the initial HZ diagnosis. Evaluating PHN risk is essential for determining the burden on patients and health-care systems, but research shows variable estimates. The extent to which these differences are related to the assessment method has not been examined. The purpose of this study is to compare the proportion of PHN among HZ patients measured by medical chart review and self-report surveys.

METHODS

PHN risk was assessed among a sample of Kaiser Permanente Southern California members with HZ. Chart reviews identified lingering pain 90-180 days post-HZ diagnosis and the Zoster Brief Pain Inventory was administered 90 days post-HZ diagnosis by telephone. Frequencies of PHN identified with each approach were cross-tabulated and stratified by sex, age group, and zoster vaccine live vaccination status.

RESULTS

Chart review and self-report were largely concordant (n=875, 89.20%); however, chart review yielded lower PHN risk overall and for the stratified subgroups. PHN from self-report was substantially higher (6.30-8.33%) among patients who were male, ≥70 years, or unvaccinated. Among those who typically seek care more often (female, younger, vaccinated), the discrepancy between each method was notably lower (1.60-2.92%).

CONCLUSION

Our findings suggest that chart review underestimates cases among those less likely to seek health care, including males, the elderly, and unvaccinated individuals. The agreement between the methods indicates that each can provide a reasonable approximation of PHN, but analyses should carefully control for health-care utilization.

Determination of Total Vitamin C in Fruit Juices and Related Products by Liquid Chromatography: Interlaboratory Study

A interlaboratory study was conducted to evaluate a liquid chromatographic (LC) procedure for the determination of total vitamin C in foods at levels of 5–60 mg/100 g. Emphasis was placed on fruit juices, although selected foods were also included in the study. Following dissolution of sample in water, endogenous dehydroascorbic acid was converted to ascorbic acid by precolumn reduction with dithiothreitol at neutral pH. Total ascorbate was determined by C18 reversed-phase LC with a phosphate eluent at pH 2.5, incorporating dithiothreitol to maintain vitamin C in the reduced form, and UV detection at 254 nm. Seven types of fruit juices and foods were tested by 19 collaborators in 7 countries. Three duplicate juices and foods met the criteria for Youden pairs and yielded repeatability relative standard deviation of 5.80–14.66%. Reproducibility relative standard deviation ranged from 6.36 to 35.54% (n = 10) with HORRAT values of 0.82–4.04. The LC method is suitable for routine use in fruit products and foods containing &gt;5 mg/100 g vitamin C and is recommended for further validation by AOAC INTERNATIONAL and International Fruit Juice Union.

Home proximity to flower plantations and higher systolic blood pressure among children

BACKGROUND

Pesticide drift from agricultural plantations increases the chemical exposure potential of people living nearby. Some studies have described positive associations between pesticide exposures and blood pressure (BP) in adults, whereas limited evidence in children suggests negative associations. This study characterized the association between home proximity to plantations and BP among children living in a flower-growing county in Ecuador.

METHODS

We included 310 4-9-year-old children living in Pedro Moncayo County, Ecuador as part of The ESPINA study. We calculated age, gender and height-specific BP z-scores. Geographic coordinates of homes and flower plantations were collected using GPS receivers and satellite imagery. Exposure-outcome associations were analyzed using linear regression.

RESULTS

The mean home distance to the nearest flower plantation was 449 m (SD: 347) and the median plantation area within 150 m of participants' homes was 989 m² (25^th-75^Th percentile: 492-3164) among those with non-zero values. Children living closer to plantations had lower AChE activity. Systolic BP z-score increased with greater residential proximity to plantations (0.24 SD per 1000 m [95% CI: 0.01, 0.47]) and with greater areas of flower plantations within 150 m of homes (0.03 SD per 1000 m² [0.00, 0.06]), after adjusting for socio-economic, anthropometric and other factors. Further adjustment for acetylcholinesterase and hemoglobin strengthened these associations.

CONCLUSIONS

Proximity of homes to flower plantations and greater plantation areas within 150 m from homes were associated with higher systolic BP, independent of cholinesterase activity. This suggests that non-cholinesterase inhibitor pesticide drift from agricultural plantations may be sufficient to induce physiologic changes on children living nearby.