Bayesian Estimation of real-time Epidemic Growth Rates using Gaussian Processes: local dynamics of SARS-CoV-2 in England

Quantitative assessments of the recent state of an epidemic and short-term projections into the near future are key public health tools that have substantial policy impacts, helping to determine if existing control measures are sufficient or need to be strengthened. Key to these quantitative assessments is the ability to rapidly and robustly measure the speed with which the epidemic is growing or decaying. Frequently, epidemiological trends are addressed in terms of the (time-varying) reproductive number R. Here, we take a more parsimonious approach and calculate the exponential growth rate, r, using a Bayesian hierarchical model to fit a Gaussian process to the epidemiological data. We show how the method can be employed when only case data from positive tests are available, and the improvement gained by including the total number of tests as a measure of heterogeneous testing effort. Although the methods are generic, we apply them to SARS-CoV-2 cases and testing in England, making use of the available high-resolution spatio-temporal data to determine long-term patterns of national growth, highlight regional growth and spatial heterogeneity.

Forecasting COVID-19 infection trends and new hospital admissions in England due to SARS-CoV-2 Variant of Concern Omicron

Objectives: On November 26, 2021, WHO designated the variant B.1.1.529 as a new SARS-CoV-2 variant of concern (VoC), named Omicron, originally identified in South Africa. Several mutations in Omicron indicate that it may have an impact on how it spreads, resistance to vaccination, or the severity of illness it causes. We used our previous modelling algorithms to forecast the spread of Omicron in England. Design: We followed EQUATOR TRIPOD guidance for multivariable prediction models. Setting: England. Participants: Not applicable. Interventions: Non-interventional, observational study with a predicted forecast of outcomes. Main outcome measures: Trends in daily COVID-19 cases with a 7-day moving average and of new hospital admissions. Methods: Modelling included a third-degree polynomial curve in existing epidemiological trends on the spread of Omicron and a new Gaussian curve to estimate a downward trend after a peak in England. Results: Up to February 15, 2022, we estimated a projection of 250,000 COVID-19 daily cases of Omicron spread in the worse scenario, and 170,000 in the best scenario. Omicron might represent a relative increase from the background daily rates of COVID-19 infection in England of mid December 2021 of 1.9 to 2.8-fold. With a 5-day lag-time, daily new hospital admissions would peak at around 5,063 on January 23, 2022 in the worse scenario. Conclusion: This warning of pandemic surge of COVID-19 due to Omicron is calling for further reinforcing in England and elsewhere of universal hygiene interventions (indoor ventilation, social distance, and face masks), and anticipating the need of new total or partial lockdowns in England.

Epidemiological trends and trajectories of MAFLD-associated hepatocellular carcinoma 2002–2033: the ITA.LI.CA database

BackgroundMetabolic dysfunction-associated fatty liver disease (MAFLD) represents a new inclusive definition of the whole spectrum of liver diseases associated to metabolic disorders. The main objective of this study was to compare patients with MAFLD and non-MAFLD with hepatocellular carcinoma (HCC) included in a nationally representative cohort.MethodsWe analysed 6882 consecutive patients with HCC enrolled from 2002 to 2019 by 23 Italian Liver Cancer centres to compare epidemiological and future trends in three subgroups: pure, single aetiology MAFLD (S-MAFLD); mixed aetiology MAFLD (metabolic and others, M-MAFLD); and non-MAFLD HCC.ResultsMAFLD was diagnosed in the majority of patients with HCC (68.4%). The proportion of both total MAFLD and S-MAFLD HCC significantly increased over time (from 50.4% and 3.6% in 2002–2003, to 77.3% and 28.9% in 2018–2019, respectively, p<0.001). In Italy S-MAFLD HCC is expected to overcome M-MAFLD HCC in about 6 years. Patients with S-MAFLD HCC were older, more frequently men and less frequently cirrhotic with clinically relevant portal hypertension and a surveillance-related diagnosis. They had more frequently large tumours and extrahepatic metastases. After weighting, and compared with patients with non-MAFLD, S-MAFLD and M-MAFLD HCC showed a significantly lower overall (p=0.026, p=0.004) and HCC-related (p<0.001, for both) risk of death. Patients with S-MAFLD HCC showed a significantly higher risk of non-HCC-related death (p=0.006).ConclusionsThe prevalence of MAFLD HCC in Italy is rapidly increasing to cover the majority of patients with HCC. Despite a less favourable cancer stage at diagnosis, patients with MAFLD HCC have a lower risk of HCC-related death, suggesting reduced cancer aggressiveness.

South African Population Immunity and Severe Covid-19 with Omicron Variant

Background We conducted a seroepidemiological survey from October 22 to December 9, 2021, in Gauteng Province, South Africa, to determine SARS-CoV-2 immunoglobulin G (IgG) seroprevalence primarily prior to the fourth wave of coronavirus disease 2019 (Covid-19), in which the B.1.1.529 (Omicron) variant is dominant. We evaluated epidemiological trends in case rates and rates of severe disease through to December 15, 2021, in Gauteng. Methods We contacted households from a previous seroepidemiological survey conducted from November 2020 to January 2021, plus an additional 10% of households using the same sampling framework. Dry blood spot samples were tested for anti-spike and anti-nucleocapsid protein IgG using quantitative assays on the Luminex platform. Daily case and death data, weekly excess deaths, and weekly hospital admissions were plotted over time. Results Samples were obtained from 7010 individuals, of whom 1319 (18.8%) had received a Covid-19 vaccine. Overall seroprevalence ranged from 56.2% (95% confidence interval [CI], 52.6 to 59.7) in children aged <12 years to 79.7% (95% CI, 77.6 to 81.5) in individuals aged >50 years. Seropositivity was 6.22-fold more likely in vaccinated (93.1%) vs unvaccinated (68.4%) individuals. Epidemiological data showed SARS-CoV-2 infection rates increased more rapidly than in previous waves but have now plateaued. Rates of hospitalizations and excess deaths did not increase proportionately, remaining relatively low. Conclusions We demonstrate widespread underlying SARS-CoV-2 seropositivity in Gauteng Province prior to the current Omicron-dominant wave, with epidemiological data showing an uncoupling of hospitalization and death rates from infection rate during Omicron circulation.

Forecasting COVID-19 infection trends in the EU-27 countries, the UK and Switzerland due to SARS-CoV-2 Variant of Concern Omicron

Background: On November 26, 2021, WHO designated the variant B.1.1.529 as a new SARS-CoV-2 variant of concern (VoC), named Omicron, originally identified in South Africa. Several mutations in Omicron indicate that it may have an impact on how it spreads, resistance to vaccination, or the severity of illness it causes. Methods: We used our previous modelling algorithms to forecast the spread of Omicron aggregated in the EU-27 countries, the United Kingdom and Switzerland, and report trends in daily cases with a 7-day moving average. We followed EQUATOR TRIPOD guidance for multivariable prediction models. Modelling included a third-degree polynomial curve in existing epidemiological trends on the spread of Omicron in South Africa, a five-parameter logistic (5PL) asymmetrical sigmoidal curve following a parametric growth in Europe, and a new Gaussian curve to estimate a downward trend after a peak. Results: Up to January 15, 2022, we estimated a background rate projection in EU-27 countries, the UK and Switzerland of about 145,000 COVID-19 daily cases without Omicron, which increases up to 440,000 COVID-19 daily cases in the worst scenario of Omicron spread, and 375,000 in the best scenario. Therefore, Omicron might represent a relative increase from the background daily rates of COVID-19 infection in Europe of 1.03-fold or 2.03-fold, that is up to a 200% increase. Conclusion: This warning pandemic surge due to Omicron is calling for further reinforcing of COVID-19 universal hygiene interventions (indoor ventilation, social distance, and face masks), and anticipating the need of new lockdowns in Europe.

Epidemiological trends in tuberculosis in Ukraine at the beginning of the COVID­-19 pandemic

Objective — to examine the tendencies of the epidemiological situation on tuberculosis in Ukraine at the beginning of the COVID-19 pandemic in 2020. Materials and methods. The analysis of the data of official statistics in 2015—2020, a survey of 157 medical experts and a telephone questionnaire survey of 69 residents of the Volyn region. Results and discussion. It was established that the disease of COVID-19 has found its imprint on the epidemiological situation of tuberculosis and on the functioning of the TB care service. In 2020, the rate of decline in the incidence of pulmonary and extrapulmonary tuberculosis was significantly more intensive than in previous years. However, the incidence of tuberculosis among contacts with bacterial excretion in tuberculosis foci increased 1.85 times in each year. The frequency of tuberculosis recurrences is steadily decreasing.The prevalence and mortality from all forms of active tuberculosis among the entire population of Ukraine has a tendency similar to a decrease in morbidity.The effectiveness of treatment of patients of all categories is proportional to the severity of the tuberculosis process, but still insufficient. Mortality in TB care institutions increased in the previous year against the decrease of this indicator in previous years. Against the background of the inaccessibility of the population to TB care, day hospitals are underused, and the sanatorium network needs to be reorganized. The surgical method of treatment of patients is extremely insufficiently realized. Conclusions. The dispensary contingent of TB care institutions is decreasing every year. There is a reduction in the infrastructure of the TB care service, and in each year, the largest reduction was in the bed stock of TB care institutions and sanatoriums, as well as a decrease in the number of TB doctors.

Surveillance and epidemiology of SARS-CoV-2 viral variants in the United States, May-October 2021 (Preprint)

UNSTRUCTURED Background: Genomic sequencing of SARS-CoV-2 positive specimens has been critical in detecting and tracking variants of concern. Methods: We analyzed a recent cohort of SARS-CoV-2-positive specimens collected from patients in over 5,000 testing locations across the United States. These data were combined with an online pre-screening questionnaire on symptoms, exposures and vaccination status to examine epidemiological trends related to virulence, transmissibility, and vaccine effectiveness. Results: Between May and October 2021, 177,253 patient specimens were sequenced and approximately 400 different SARS-CoV-2 lineages identified. Within this cohort, 152,373 (86.0%) were aged 16 and older, and the percent of these patients that were fully vaccinated increased from 4.5% in May to 42.3% in October. Although positivity rates of fully vaccinated patients increased, unvaccinated patients were 30.4% (95% CI 26.5-34.3%) more likely to report shortness of breath and 34.0% (95% CI 32.1-35.9%) more likely to report fever, shaking, or chills. Conclusions: Our nationally representative database of patient-reported measures and lineage data from SARS-CoV-2 specimens provides useful data to track emerging trends and lineages of concern.