Eurosurveillance - Volume 26, Issue 9, 04 March 2021

Whole genome sequencing (WGS) is increasingly used for pathogen identification and surveillance.

We evaluated costs and benefits of routine WGS through case studies at eight reference laboratories in Europe and the Americas which conduct pathogen surveillance for avian influenza (two laboratories), human influenza (one laboratory) and food-borne pathogens (five laboratories).

The evaluation focused on the institutional perspective, i.e. the ‘investment case’ for implementing WGS compared with conventional methods, based on costs and benefits during a defined reference period, mostly covering at least part of 2017. A break-even analysis estimated the number of cases of illness (for the example of Salmonella surveillance) that would need to be avoided through WGS in order to ‘break even’ on costs.

On a per-sample basis, WGS was between 1.2 and 4.3 times more expensive than routine conventional methods. However, WGS brought major benefits for pathogen identification and surveillance, substantially changing laboratory workflows, analytical processes and outbreaks detection and control. Between 0.2% and 1.1% (on average 0.7%) of reported salmonellosis cases would need to be prevented to break even with respect to the additional costs of WGS.

Even at cost levels documented here, WGS provides a level of additional information that more than balances the additional costs if used effectively. The substantial cost differences for WGS between reference laboratories were due to economies of scale, degree of automation, sequencing technology used and institutional discounts for equipment and consumables, as well as the extent to which sequencers are used at full capacity.

Several clinical trials have assessed the protective potential of chloroquine and hydroxychloroquine. Chronic exposure to such drugs might lower the risk of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or severe coronavirus disease (COVID-19).

To assess COVID-19 incidence and risk of hospitalisation in a cohort of patients chronically taking chloroquine/hydroxychloroquine.

We used linked health administration databases to follow a cohort of patients with chronic prescription of hydroxychloroquine/chloroquine and a control cohort matched by age, sex and primary care service area, between 1 January and 30 April 2020. COVID-19 cases were identified using International Classification of Diseases 10 codes.

We analysed a cohort of 6,746 patients (80% female) with active prescriptions for hydroxychloroquine/chloroquine, and 13,492 controls. During follow-up, there were 97 (1.4%) COVID-19 cases in the exposed cohort and 183 (1.4%) among controls. The incidence rate was very similar between the two groups (12.05 vs 11.35 cases/100,000 person-days). The exposed cohort was not at lower risk of infection compared with controls (hazard ratio (HR): 1.08; 95% confidence interval (CI): 0.83–1.44; p = 0.50). Forty cases (0.6%) were admitted to hospital in the exposed cohort and 50 (0.4%) in the control cohort, suggesting a higher hospitalisation rate in the former, though differences were not confirmed after adjustment (HR: 1·46; 95% CI: 0.91–2.34; p = 0.10).

Patients chronically exposed to chloroquine/hydroxychloroquine did not differ in risk of COVID-19 nor hospitalisation, compared with controls. As controls were mainly female, findings might not be generalisable to a male population.

Swedish hepatitis A surveillance includes sequence-based typing, but its contribution to outbreak detection in relation to epidemiological investigations has not been fully evaluated.

To evaluate the role of sequence-based typing in hepatitis A outbreak detection and to describe the hepatitis A epidemiology in Sweden to improve surveillance.

We retrospectively investigated hepatitis A virus sequences of 447 cases notified in Sweden 2009–18. We performed a phylogenetic analysis of evolutionary distances to identify cases with similar virus sequences (≥ 459/460 identical nt in the VP1/P2A junction). Unique sequences, dyads and sequence-based clusters (SBCs) were identified. We linked non-sequenced cases by epidemiological information and retrospectively assessed the value of typing for outbreak identification.

Fifty-five percent (n = 542/990) of the notified hepatitis A cases were referred to the Public Health Agency of Sweden for typing and 447 (45%) were sequenced successfully. Subgenotypes included IA (42.5%, n = 190), IB (42.7%, n = 191) and IIIA (14.8%, n = 66). Phylogenetic analysis identified 154 unique sequences, 33 dyads (66 cases) and 34 SBCs (227 cases). The combination of molecular and epidemiological data revealed 23 potential outbreaks comprising 201 cases. Cases were linked by sequence (59%, n = 118), epidemiological data (11%, n = 23) or both (30%, n = 60). Typing was needed to identify 15 of 23 potential outbreak signals.

Sequence-based typing contributed substantially to detecting clustering cases and identifying outbreaks in Sweden. The results show routine sequence-based typing detects outbreaks, promotes timely outbreak investigations and facilitates international collaboration.