Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, Portugal

We estimated comparative primary and booster vaccine effectiveness (VE) of SARS-CoV-2 Omicron BA.5 and BA.2 lineages against infection and disease progression. During April-June 2022, we implemented a case-case and cohort study and classified lineages using whole-genome sequencing or spike gene target failure. For the case-case study, we estimated the adjusted odds ratios (aORs) of vaccination using a logistic regression. For the cohort study, we estimated VE against disease progression using a penalized logistic regression. We observed no reduced VE for primary (aOR 1.07 [95% CI 0.93-1.23]) or booster (aOR 0.96 [95% CI 0.84-1.09]) vaccination against BA.5 infection. Among BA.5 case-patients, booster VE against progression to hospitalization was lower than that among BA.2 case-patients (VE 77% [95% CI 49%-90%] vs. VE 93% [95% CI 86%-97%]). Although booster vaccination is less effective against BA.5 than against BA.2, it offers substantial protection against progression from BA.5 infection to severe disease.

Real-time classification of causes death using Artificial Intelligence – sensitivity analysis

Background

Last year Europe registered >365 000 excess deaths, most from preventable causes. In order to timely track deaths, the Portuguese Directorate-General of Health developed a deep neural network that codifies ICD-10 causes of death (AUTOCOD) by analyzing free text in a death certificate (DC). While the performance of AUTOCOD has been demonstrated, it was not clear if it was sustained during excess mortality periods, when text quality could be lower due to the increased pressure on health services.

Methods

We performed a sensitivity analysis comparing the ICD-10 classifications of 330 098 Portuguese DC by AUTOCOD and by human-coders, from 2016 to 2019. Excess mortality was defined using the EuroMOMO methodology and a sub-analysis in periods of extreme excess (+4 and +6 SD). We compared the periods without excess mortality with the periods of excess and extreme mortality by chapter. The same analysis was performed for ICD-10 blocks, for the three most common chapters (neoplasms; diseases circulatory and respiratory system). The confusion matrixes allowed us to calculate AUTOCOD's performance metrics, like sensitivity.

Results

AUTOCOD showed high sensitivity (≥0.75) in 10 chapters, with values above 0.90 for the three most common ones. The weighted-average of sensitivity showed no difference between periods without excess mortality and periods of excess mortality, a difference of 0.01 for periods of extreme mortality (+4 SD) and a difference of 0.04 for periods of extreme mortality (+6 SD). For the block classification, performance was similar.

Conclusions

Even in periods of excess and extreme mortality, AUTOCOD accurately predicts the classification of the cause of death. Meaning that it is not affected by a potential loss in text-quality due to pressure in health services. This allows for the use of AUTOCOD for real time mortality surveillance and it highlights the importance of Artificial Intelligence as an advisory tool for Public Health policies in emergencies.

Key messages

• Artificial Intelligence algorithms like AUTOCOD can predict the ICD-10 cause of death with very high sensitivity, during periods with and without excess mortality.

• Artificial Intelligence algorithms like AUTOCOD can be used for real-time cause specific mortality surveillance, providing valuable information for policy making during periods of excess mortality.

Rapid waning of protection induced by prior BA.1/BA.2 infection against BA.5 infection

SARS-CoV-2 omicron subvariants BA.1 and BA.2 became dominant in many countries in early 2022. These subvariants are now being displaced by BA.4 and BA.5. While natural infection with BA.1/BA.2 provides some protection against BA.4/BA.5 infection, the duration of this protection remains unknown. We used the national Portuguese COVID-19 registry to investigate the waning of protective immunity conferred by prior BA.1/BA.2 infection towards BA.5. We divided the individuals infected during the period of BA.1/BA.2 dominance (>90% of sample isolates) in successive 15-day intervals and determined the risk of subsequent infection with BA.5 over a fixed period. Compared with uninfected people, one previous infection conferred substantial protection against BA.5 re-infection at 3 months (RR=0.12; 95% CI: 0.11-0.12). However, although still significant, the protection was reduced by two-fold at 5 months post-infection (RR=0.24; 0.23-0.24). These results should be interpreted in the context of vaccine breakthrough infections, as the vaccination coverage in the individuals included in the analyses is >98% since the end of 2021. This waning of protection following BA.1/BA.2 infection highlights the need to assess the stability and durability of immune protection induced with the adapted vaccines (based on BA.1) over time.

Ongoing monkeypox virus outbreak, Portugal, 29 April to 23 May 2022

Up to 27 May 2022, Portugal has detected 96 confirmed cases of monkeypox. We describe 27 confirmed cases (median age: 33 years (range: 22-51); all males), with an earliest symptom onset date of 29 April. Almost all cases (n = 25) live in the Lisbon and Tagus Valley health region. Most cases were neither part of identified transmission chains, nor linked to travel or had contact with symptomatic persons or with animals, suggesting the possible previously undetected spread of monkeypox.

Increasing risk of breakthrough COVID-19 in outbreaks with high attack rates in European long-term care facilities, July to October 2021

We collected data from 10 EU/EEA countries on 240 COVID-19 outbreaks occurring from July−October 2021 in long-term care facilities with high vaccination coverage. Among 17,268 residents, 3,832 (22.2%) COVID-19 cases were reported. Median attack rate was 18.9% (country range: 2.8–52.4%), 17.4% of cases were hospitalised, 10.2% died. In fully vaccinated residents, adjusted relative risk for COVID-19 increased with outbreak attack rate. Findings highlight the importance of early outbreak detection and rapid containment through effective infection prevention and control measures.

Initial assessment of the COVID-19 vaccination's impact on case numbers, hospitalisations and deaths in people aged 80 years and older, 15 EU/EEA countries, December 2020 to May 2021

Prioritisation of elderly people in COVID-19 vaccination campaigns aimed at reducing severe outcomes in this group. Using EU/EEA surveillance and vaccination uptake, we estimated the risk ratio of case, hospitalisation and death notifications in people 80 years and older compared with 25-59-year-olds. Highest impact was observed for full vaccination uptake 80% or higher with reductions in notification rates of cases up to 65% (IRR: 0.35; 95% CI: 0.13-0.99), hospitalisations up to 78% (IRR: 0.22; 95% CI: 0.13-0.37) and deaths up to 84% (IRR: 0.16; 95% CI: 0.13-0.20).

Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021

We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8).

Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021

We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with the odds of B.1.1.7 proportion increasing at an estimated 89% (95% confidence interval: 83-95%) per week until week 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track B.1.1.7 spread, besides the spike gene target failure (SGTF) proxy. SGTL/SGTF samples were associated with statistically significant higher viral loads, but not with substantial shift in age distribution compared to non-SGTF/SGTL cases.

No country for old men: gender disparities in Portuguese mortality

Background

Portugal is divided into 25 NUTS 3 (Nomenclature of Territorial Units for Statistics). Mortality tracking is one of the core elements of SDG3 indicators. It can also be used as an essential metric to SDG5 on gender disparities. This study looked into gender disparities in mortality in Portugal.

Methods

We used data from Statistics Portugal, precisely the standardized rate of potential years of life lost per 100 000 inhabitants to all causes of death using the standard European population by gender. We subdivided by NUTS 3 and we have plotted PYLL for males, females, and the difference between both for the year 2018 using ArcMap 10.7.1. Further descriptive analysis was conducted in R 3.61 and Rstudio 1.2.5033.

Results

We have found significant gender disparities in mortality. These gender disparities afflicted men the most. In 88% of NUTS3, the PYLL difference of more than 2000 years/100000 when comparing men with women. The higher disparities were in the Azores, Alto Tâmega, and the Douro. Some of the critical specific causes of mortality that lead to this disparity are malignant tumors, mental health problems, alcohol abuse, circulatory system diseases, accidents, and suicides.

Conclusions

We have found that there are significant disparities in gender mortality targeting men. Although it is higher in some Portuguese regions, the problem is widespread. Further research is needed to address the causes of gender disparity in health outcomes in Portugal.

Key messages

Huge gap in YPLL between men and women, starting an young adult age. The urgent need for health programs that target men health problems.