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Infectiousness of SARS-CoV-2 infections and reinfections during the Omicron wave

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Using detailed epidemiological data from SARS-CoV-2 surveillance in the California state prison system, we found that vaccination and prior infection reduced the infectivity of SARS-CoV-2 infections during an Omicron dominance (subvariants BA.1 and BA.2) period. Vaccination and prior infection were associated with similar reductions in infectivity during SARS-CoV-2 infection, and notably, additional vaccination doses (e.g., booster doses) against SARS-CoV-2 and more recent vaccination led to greater reductions in infectivity. It is important to note that the reductions in transmission risk associated with both vaccination and prior infection were additive, indicating an increased benefit conferred by vaccination to reduce the infectivity of cases, even after prior infection. Regardless of prior vaccination and/or natural infection, SARS-CoV-2 infections and reinfections remained highly infectious and accounted for 80% of the transmission observed in the study population, which has high levels of prior infection and vaccination. This observation underscores that vaccination and naturally acquired predominant immunity alone do not eliminate the risk of SARS-CoV-2 infection, especially in high-risk settings such as prisons.

Previous studies during the Delta variant wave and before widespread booster vaccination are mixed on whether SARS-CoV-2 infections in vaccinated individuals are potentially less infectious6,7,8 or equally infectious9.10 to primary infections. In more recent household contact studies during the Omicron variant era11, 12, 13, vaccination generally leads to reduced infectivity of SARS-CoV-2. Several factors may have enhanced our ability to observe statistically significant findings in the present study. The risk of transmission between close contacts in the prison environment and the consistency in contact structure, especially in light of the increased transmissibility of the Omicron SARS-CoV-2 variant, may have increased statistical power in our sample. Likewise, a greater proportion of index cases in our sample were previously vaccinated or infected, further increasing the opportunity to compare the transmission risk of vaccinated or unvaccinated index cases and those who were previously infected or uninfected.

An important result is that the vaccine-mediated reduction in infectivity of SARS-CoV-2 infections appears to be dose-dependent. Each vaccine dose provided an additional 11% average relative reduction in infectivity, which was driven primarily by residents receiving a booster dose. Findings from this study support indirect effects of COVID-19 vaccination (especially booster shots) to delay transmission of SARS-CoV-2 and build on evidence of direct effects of COVID-19 vaccination23 to emphasize the overall importance of vaccination against COVID-19. The public health implication of these findings is further support for existing policy using booster vaccinations.24 to achieve the goal of reducing transmission at the population level. The impact of additional doses of bivalent vaccine, now authorized for individuals over 5 to 6 years of age25, in transmission should be a priority for further study. Additional considerations regarding the timing of vaccine doses are also warranted, as we found that index cases with the most distant history of COVID-19 vaccination were at increased risk of transmitting the infection to close contacts. In light of this finding, this study raises the possibility of scheduled mass vaccination in incarcerated settings during outbreaks to delay transmission.

The findings of this study have direct implications for addressing COVID-19 inequalities in the prison population through additional vaccination. In California state prisons at the time of this study, although 81% of residents and 73% of staff completed a primary vaccination series, only 59% of residents and 41% of staff received the number of vaccination doses recommended by the Centers for Disease control and prevention based on age and medical comorbidities26. Our findings also provide a basis for further consideration for case-housing situations based on prior vaccination and infection history in future outbreaks, and can be used alongside other measures, such as depopulation and ventilation interventions, to protect incarcerated populations.

However, this study also underscores the persistent vulnerability to COVID-19 among residents and staff in correctional settings despite widespread vaccination, natural immunity, and use of non-pharmaceutical interventions. The overall SARS-CoV-2 attack rate in the study population (which was usually isolated after symptoms or a positive test) was 30%, and index cases with advanced infections or reinfections remained highly infectious, which calls into question the ability to high vaccination rates alone to prevent all transmission of SARS-CoV-2 in correctional settings. In the United States, which incarcerates more residents per capita than any other country in the world26 and has a quarter of the world’s incarcerated population, correctional settings are characterized by poorly ventilated facilities, populations with increased rates of comorbid health conditions, high-risk dormitories, and overcrowding18, 27, 28, 29. Given the inability of current efforts to reduce SARS-CoV-2 transmission, extrication efforts may be the most likely to have substantial effects in reducing cases.

The secondary attack rate in this study was at the lower end of published estimates when compared to domestic studies. It is important to note that the secondary attack rate of the SARS-CoV-2 Omicron variant in recent domestic studies ranges from 29% to 53%.11, 12, 13, in contrast to a 30% attack rate in this study. The prison environment presents distinct epidemiological differences in relation to households. The dense living environment increases the likelihood of transmission in the prison environment compared to a household, while frequent asymptomatic testing (with isolation of positive cases) in prisons likely reduced exposure time and the risk of subsequent transmission compared to households . Prison cell transmission is also probably more uniform than a family.

Strengths of this study include access to detailed records of all residents in the State of California prison system, covering the subjects’ prior receipt of the COVID-19 vaccine and past natural infection history (based on frequent testing during the pandemic). ), as well as a social network provided a record of where residents slept each night during the study period. We used a consistent definition of social contact between the COVID-19 index case and close contact based on uniformity of cell type. Frequent testing ensures early identification of infections and systematic capture of asymptomatic and symptomatic infections to avoid bias by participants’ immune status (which can affect temporal onset of symptoms). The risk of misclassifying close contacts is low, as most follow-up testing in close contacts has occurred well after the first exposure to an index case (Further Notes). The large sample size facilitates analyzes of the contribution of combinations of prior vaccination status and natural infection to transmission risk, including analyzes examining the impact of booster doses.

Limitations must also be considered. We cannot exclude the possibility of some residual confounding (eg, behavioral differences that affect transmission risk) between individuals who were vaccinated against SARS-CoV-2 and those who were not vaccinated. There is a possibility that close contacts who test positive for SARS-CoV-2 were not infected by the assigned index case, but rather through interaction with infectious individuals outside their cell. However, this misattribution is expected to lessen the apparent associations of transmission risk with the vaccination status and infection history of the index cases, but not overturn the relative estimates. To further address the risk of misattribution, we adjusted for background SARS-CoV-2 incidence and matched contact pairs by facility and time. Our study population is a subset of the entire California prison population and may not represent all prison settings. SARS-CoV-2 infectiousness studies may be subject to bias30, 31, 32. The strict inclusion and exclusion criteria in this study may introduce bias in the analysis, although we performed sensitivity analyzes on these criteria with generally consistent results. We also adjusted for prior infection in the analyzes to account for potential concerns about differential susceptibility related to prior infection in vaccinated versus unvaccinated individuals. Given the limited capacity for SARS-CoV-2 testing early in the pandemic and the decision of some residents to decline testing, it is possible that infections among some residents were not captured, although such misclassification is expected to come from our findings. to null. Testing for SARS-CoV-2 has varied over time in the prison system, with periods of routine weekly testing and other periods of reactive testing; however, periods without reactive testing do line up with periods during which SARS-CoV-2 was unlikely to circulate at high levels within facilities, suggesting that this is unlikely to substantially affect the results. The study’s findings on boosters may also be related to recent effects of vaccination. This study design did not provide a basis for identifying the effects of vaccination and prior infection on the risk of acquiring SARS-CoV-2 among close contacts, although we made adjustments for prior infection and vaccination in close contacts in the primary analysis. It is noteworthy that vaccine efficacy against the infection among incarcerated persons has been reported in this population during earlier periods.33.34. We do not have a detailed record of masking at the person level, symptoms, cycle limits for polymerase chain reaction (PCR) testing or serological testing. During the study, the predominant Omicron subvariants in California and California prisons were BA.1 and BA.2 based on genomic surveillance, although we did not genotype all SARS-CoV-2 isolates in this study.

This study demonstrates that breakthrough COVID-19 infections with the Omicron variant remain highly infectious, but both vaccination and natural infection confer reductions in transmission, with the benefit of additional doses of vaccine. As SARS-CoV-2 infections and reinfections become the predominant case of COVID-19, this study supports the importance of booster doses in reducing transmission at a population level, considering mass vaccination during outbreaks, with particular relevance in vulnerable areas and high-density congregation settings.