Transmission potential of vaccinated and unvaccinated persons infected with the SARS-CoV-2 Delta variant in a federal prison, July-August 2021

Data-driven mathematical modeling approaches for COVID-19: A survey

In this review, we successively present the methods for phenomenological modeling of the evolution of reported and unreported cases of COVID-19, both in the exponential phase of growth and then in a complete epidemic wave. After the case of an isolated wave, we present the modeling of several successive waves separated by endemic stationary periods. Then, we treat the case of multi-compartmental models without or with age structure. Eventually, we review the literature, based on 260 articles selected in 11 sections, ranging from the medical survey of hospital cases to forecasting the dynamics of new cases in the general population. This review favors the phenomenological approach over the mechanistic approach in the choice of references and provides simulations of the evolution of the number of observed cases of COVID-19 for 10 states (California, China, France, India, Israel, Japan, New York, Peru, Spain and United Kingdom).

Indirect vaccine effectiveness in an outbreak of Alpha B.1.1.7 variant in a California state Prison, May 2021

Incarcerated populations experienced high rates of SARS-CoV-2 infection and death during early phases of the COVID-19 pandemic. To evaluate vaccine effectiveness in the carceral context, we investigated the first outbreak of COVID-19 in a California state prison following widespread rollout of vaccines to residents in early 2021. We identified a cohort of 733 state prison residents presumed to be exposed between May 14 and June 22, 2021. 46.9 % (n = 344) were vaccinated, primarily with two doses of mRNA-1273 (n = 332, 93.6 %). In total, 92 PCR-positive cases were identified, of which 14 (14.5 %) occurred among mRNA-1273 vaccinated residents. No cases required hospitalization. All nine isolates collected belonged to the Alpha (B.1.1.7) variant. We used Cox proportional hazard regression to estimate vaccine effectiveness for at least one dose of any vaccine at the start of the outbreak. Vaccine effectiveness was 86 % (95 % CI: 75 %-97 %) against PCR-confirmed infection, with similar results for symptomatic infection. Higher rates of building-level vaccine uptake were associated with a lower overall rate of PCR-confirmed infection and symptomatic infection among unvaccinated residents. Among unvaccinated residents who lived in shared cells at the time of presumed exposure, exposure to a vaccinated cellmate was associated with a 38% (95% CI: 0.37, 1.04) lower hazard rate of PCR-confirmed infection over the study period. In this outbreak involving the Alpha SARS-CoV-2 variant, vaccination conferred direct and possibly indirect protection against SARS-CoV-2 infection and symptomatic COVID-19. Our results support the importance of vaccine uptake in mitigating outbreaks and severe disease in the prison setting and the consideration of community vaccination levels in policy and infection response.

Duration of SARS-CoV-2 shedding: A systematic review

Background

Positive viral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cultures indicate shedding of infectious virus and corresponding transmission risk of coronavirus disease 2019 (COVID-19). The research question of this systematic review was: Is there a discernible pattern in the timing of SARS-CoV-2 virus isolation, and what is the proportion of positive and negative results for isolation of SARS-CoV-2 virus with viral culture relative to the onset of clinical symptoms or the day of diagnosis, as indicated by longitudinal studies?

Methods

We systematically searched PubMed and Embase from inception to 16 February 2023 for English-language studies with serial viral culture testing within symptomatic or asymptomatic SARS-CoV-2 infected persons during the post-vaccination period. Outcomes of interest were the daily culture status per study and the overall daily culture positivity rate of SARS-CoV-2. We critically appraised the selected studies using the Newcastle-Ottawa quality assessment scale.

Results

We included 14 viral shedding studies in this systematic review. Positive viral SARS-CoV-2 cultures were detected in samples ranging from 4 days before to 18 days after symptom onset. The daily culture SARS-CoV-2 positivity rate since symptom onset or diagnosis showed a steep decline between day 5 and 9, starting with a peak ranging from 44% to 50% on days -1 to 5, decreasing to 28% on day 7 and 11% on day 9, and finally ranging between 0% and 8% on days 10-17.

Conclusions

Viral shedding peaked within 5 days since symptom onset or diagnosis and the culture positivity rate rapidly declined hereafter. This systematic review provides an overview of current evidence on the daily SARS-CoV-2 culture positivity rates during the post-vaccination period. These findings could be used to estimate the effectiveness of public health control measures, including treatment and preventive strategies, to reduce the spread of COVID-19.

Reconstructing the COVID-19 incidence in India using airport screening data in Japan

BACKGROUND

A major epidemic of COVID-19 caused by the Delta variant (B.1.617.2) occurred in India from March to July 2021, resulting in 19 million documented cases. Given the limited healthcare and testing capacities, the actual number of infections is likely to have been greater than reported, and several modelling studies and excess mortality research indicate that this epidemic involved substantial morbidity and mortality.

METHODS

To estimate the incidence during this epidemic, we used border entry screening data in Japan to estimate the daily incidence and cumulative incidence of COVID-19 infection in India. Analysing the results of mandatory testing among non-Japanese passengers entering Japan from India, we calculated the prevalence and then backcalculated the incidence in India from February 28 to July 3, 2021.

RESULTS

The estimated number of infections ranged from 448 to 576 million people, indicating that 31.8% (95% confidence interval (CI): 26.1, 37.7) - 40.9% (95% CI: 33.5, 48.4) of the population in India had experienced COVID-19 infection from February 28 to July 3, 2021. In addition to obtaining cumulative incidence that was consistent with published estimates, we showed that the actual incidence of COVID-19 infection during the 2021 epidemic in India was approximately 30 times greater than that based on documented cases, giving a crude infection fatality risk of 0.47%. Adjusting for test-negative certificate before departure, the quality control of which was partly questionable, the cumulative incidence can potentially be up to 2.3-2.6 times greater than abovementioned estimates.

CONCLUSIONS

Our estimate of approximately 32-41% cumulative infection risk from February 28 to July 3, 2021 is roughly consistent with other published estimates, and they can potentially be greater, given an exit screening before departure. The present study results suggest the potential utility of border entry screening data to backcalculate the incidence in countries with limited surveillance capacity owing to a major surge in infections.