SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic

BACKGROUND

The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022.

METHODS

We sequenced a total of 27,550 SARS-CoV-2 samples in Estonia between March 2020 and March 2022. High-quality sequences were genotyped and assigned to Nextstrain clades and Pango lineages. We used regression analysis to determine the dynamics of lineage diversity and the probability of clade-specific hospitalisation stratified by age and sex.

RESULTS

We successfully sequenced a total of 25,375 SARS-CoV-2 genomes (or 92%), identifying 19 Nextstrain clades and 199 Pango lineages. In 2020 the most prevalent clades were 20B and 20A. The various subsequent waves of infection were driven by 20I (Alpha), 21J (Delta) and Omicron clades 21K and 21L. Lineage diversity via the Shannon index was at its highest during the Delta wave. About 3% of sequenced SARS-CoV-2 samples came from hospitalised individuals. Hospitalisation increased markedly with age in the over-forties, and was negligible in the under-forties. Vaccination decreased the odds of hospitalisation in over-forties. The effect of vaccination on hospitalisation rates was strongly dependent upon age but was clade-independent. People who were infected with Omicron clades had a lower hospitalisation likelihood in age groups of forty and over than was the case with pre-Omicron clades regardless of vaccination status.

CONCLUSIONS

COVID-19 disease waves in Estonia were driven by the Alpha, Delta, and Omicron clades. Omicron clades were associated with a substantially lower hospitalisation probability than pre-Omicron clades. The protective effect of vaccination in reducing hospitalisation likelihood was independent of the involved clade.

Sharp increase in gonorrhoea notifications among young people, EU/EEA, July 2022 to June 2023

Gonorrhoea cases increased steeply in women aged 20 to 24 years across 15 EU/EEA countries in July to December 2022 and January to June 2023 with, respectively, 73% and 89% more cases reported than expected, based on historical data from 2015 to 2019. Smaller increases among men due to heterosexual transmission were observed in nine EU/EEA countries. Interventions to raise awareness among young people about sexually transmitted infection risks are needed, emphasising the benefit of safe sexual practices and testing.

Improving preparedness to respond to cross-border hepatitis A outbreaks in the European Union/European Economic Area: towards comparable sequencing of hepatitis A virus

Introduction

Sequence-based typing of hepatitis A virus (HAV) is important for outbreak detection, investigation and surveillance. In 2013, sequencing was central to resolving a large European Union (EU)-wide outbreak related to frozen berries. However, as the sequenced HAV genome regions were only partly comparable between countries, results were not always conclusive.

Aim

The objective was to gather information on HAV surveillance and sequencing in EU/European Economic Area (EEA) countries to find ways to harmonise their procedures, for improvement of cross-border outbreak responses.

Methods

In 2014, the European Centre for Disease Prevention and Control (ECDC) conducted a survey on HAV surveillance practices in EU/EEA countries. The survey enquired whether a referral system for confirming primary diagnostics of hepatitis A existed as well as a central collection/storage of hepatitis A cases’ samples for typing. Questions on HAV sequencing procedures were also asked. Based on the results, an expert consultation proposed harmonised procedures for cross-border outbreak response, in particular regarding sequencing. In 2016, a follow-up survey assessed uptake of suggested methods.

Results

Of 31 EU/EEA countries, 23 (2014) and 27 (2016) participated. Numbers of countries with central collection and storage of HAV positive samples and of those performing sequencing increased from 12 to 15 and 12 to 14 respectively in 2016, with all countries typing an overlapping fragment of 218 nt. However, variation existed in the sequenced genomic regions and their lengths.

Conclusions

While HAV sequences in EU/EEA countries are comparable for surveillance, collaboration in sharing and comparing these can be further strengthened.

Missed opportunities for HIV testing in people diagnosed with HIV, Estonia, 2014 to 2015

Background

Studies of missed opportunities for earlier diagnosis of HIV have shown that patients with undiagnosed HIV often present to healthcare settings numerous times before eventually receiving their diagnosis.

Aim

The aim of the study was to assess missed opportunities for HIV testing among people newly diagnosed with HIV.

Methods

In this observational retrospective study, we collected data from the Estonian Health Board on new HIV cases in people aged 16–49 years diagnosed in 2014–15 and from the Estonian Health Insurance Fund database for treatment invoices on their contacts with healthcare services in the 2 years preceding diagnosis. Diagnoses on treatment invoices were categorised as HIV indicator conditions using ICD-10 codes.

Results

Of 538 newly diagnosed HIV cases (62.5%; 336 men), 82% had visited healthcare services at least once during the 2 years before HIV diagnosis; the mean number of visits was 9.1. Of these, 16% had been tested for HIV and 31% had at least one ICD-10 code for an HIV indicator condition on at least one of their treatment invoices. In 390 cases of HIV indicator conditions, only 5% were tested for HIV. Of all new HIV cases aged 20–49 years from high-incidence regions (defined as priority groups in national testing guidance), 18% had been tested.

Conclusions

The HIV testing rate in the 2 years before an HIV diagnosis was very low, even in the presence of an HIV indicator condition. This emphasises the importance of implementing the Estonian HIV testing guidelines.

Standardising surveillance of hepatitis E virus infection in the EU/EEA: A review of national practices and suggestions for the way forward

BACKGROUND

Hepatitis E virus (HEV) infection is not notifiable at EU/EEA level, therefore surveillance relies on national policies only. Between 2005 and 2015, more than 20,000 cases were reported in EU/EEA countries. HEV testing is established in 26 countries and 19 countries sequence HEV viruses.

OBJECTIVE AND STUDY DESIGN

WHO's European Action plan for viral hepatitis recommends harmonised surveillance objectives and case definitions. ECDC's HEV expert group developed minimal and optimal criteria for national hepatitis E surveillance to support EU/EEA countries in enhancing their capacity and to harmonise methods.

RESULTS

The experts agreed that the primary objectives of national surveillance for HEV infections should focus on the basic epidemiology of the disease: to monitor the incidence of acute cases and chronic infections. The secondary objectives should be to describe viral phylotypes or subtypes and to identify potential clusters/outbreaks and possible routes of transmission. Seventeen of 20 countries with existing surveillance systems collect the minimal data set required to describe the epidemiology of acute cases. Eleven countries test for chronic infections. Twelve countries collect data to identify potential clusters/outbreaks and information on possible routes of transmission.

DISCUSSION

Overall, the majority of EU/EEA countries collect the suggested data and meet the outlined requirements to confirm an acute case.