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During the SARS-CoV-2 pandemic, many countries directed substantial resources toward genomic surveillance to detect and track viral variants. There is a debate over how much sequencing effort is necessary in national surveillance programs for SARS-CoV-2 and future pandemic threats. We aimed to investigate the effect of reduced sequencing on surveillance outcomes in a large genomic data set from Switzerland, comprising more than 143k sequences. We employed a uniform downsampling strategy using 100 iterations each to investigate the effects of fewer available sequences on the surveillance outcomes: (i) first detection of variants of concern (VOCs), (ii) speed of introduction of VOCs, (iii) diversity of lineages, (iv) first cluster detection of VOCs, (v) density of active clusters, and (vi) geographic spread of clusters. The impact of downsampling on VOC detection is disparate for the three VOC lineages, but many outcomes including introduction and cluster detection could be recapitulated even with only 35% of the original sequencing effort. The effect on the observed speed of introduction and first detection of clusters was more sensitive to reduced sequencing effort for some VOCs, in particular Omicron and Delta, respectively. A genomic surveillance program needs a balance between societal benefits and costs. While the overall national dynamics of the pandemic could be recapitulated by a reduced sequencing effort, the effect is strongly lineage-dependent-something that is unknown at the time of sequencing-and comes at the cost of accuracy, in particular for tracking the emergence of potential VOCs.IMPORTANCESwitzerland had one of the most comprehensive genomic surveillance systems during the COVID-19 pandemic. Such programs need to strike a balance between societal benefits and program costs. Our study aims to answer the question: How would surveillance outcomes have changed had we sequenced less? We find that some outcomes but also certain viral lineages are more affected than others by sequencing less. However, sequencing to around a third of the original effort still captured many important outcomes for the variants of concern such as their first detection but affected more strongly other measures like the detection of first transmission clusters for some lineages. Our work highlights the importance of setting predefined targets for a national genomic surveillance program based on which sequencing effort should be determined. Additionally, the use of a centralized surveillance platform facilitates aggregating data on a national level for rapid public health responses as well as post-analyses., Competing Interests: The authors declare no conflict of interest.

Switzerland is aiming to eliminate measles, in line with the objectives of the World Health Organization (WHO). Physicians, laboratories and public health authorities have made great efforts to reach this goal. A continually increasing measles vaccination coverage and other preventive measures have made an impact: no major measles outbreak has been recorded since 2011. In order to evaluate progress towards elimination, measles epidemiology of a previous epidemic period (2007–2011) was compared with the current post-epidemic period (2012–July 2018) by analysis of data from the mandatory notification system. A decrease of 94% in the average annual incidence rate occurred between the two periods (from 133 to 9 cases per million inhabitants). This was accompanied by significant changes in the epidemiology that are expected and characteristic of countries with limited circulation of the measles virus. After analysing the performance of the Swiss surveillance system and the data provided, the WHO concluded that endemic measles transmission was interrupted in Switzerland in 2016 and 2017.

With an estimated antibody prevalence of 0.7% in the low-risk population, hepatitis C virus (HCV) endemicity in Switzerland is low. We reviewed data from mandatory hepatitis C surveillance for 1988-2015 in order to describe the evolution of acute HCV infections and newly reported non-acute cases, and their epidemiological features. Crude and stratified annual incidence and notification rates and rate ratios were calculated using Poisson regression. Acute HCV incidence peaked in 2002 at 1.8 cases per 100,000 population, then declined sharply, levelling at around 0.7/100,000 from 2006. Notification rates for non-acute HCV cases peaked in 1999 (38.6/100,000), decreasing to 16.8/100,000 in 2015. Men constituted 65.5% of acute cases and 60.4% of non-acute cases. During the periods 1992-1995 and 2012-2015, the median age of acute cases increased from 28 to 37 and of non-acute cases from 32 to 48 years. The exposure leading to most acute (90.4%) and non-acute (71.9%) cases was presumably in Switzerland. Despite a sharp decrease since 2000, injecting drugs was the main reported exposure for both acute (63.8%) and non-acute (66.6%) cases, with a known exposure, followed by sexual contact with an infected person (18.9% and 10.3% respectively). Among all acute cases, the number of men who have sex with men increased sharply after the mid-2000s, totalling 41 during 2012-2015 (25.7%). Although the HCV epidemic peaked in 2000 - probably as a result of measures to control iatrogenic and percutaneous transmission - Switzerland must maintain prevention and surveillance.

Question Under Study: In July 2014, an outbreak of Salmonella enterica ssp. enterica serovar Bovismorbificans was detected in Switzerland. The goal of the outbreak investigation was to rapidly identify and eliminate the contamination source in order to prevent new cases., Methods: A case-case study design was applied comprising reported cases of S. Bovismorbificans and cases of other serovars. A trawling questionnaire was administered by telephone interview. Data were collected for 34 cases (20 S. Bovismorbificans and 14 Salmonella spp.) pertaining to food consumption during the 72 hours prior to symptom onset., Results: A statistically significant association between an S. Bovismorbificans infection and the consumption of 'salads' (odds ratio [OR] 14.3, 95% confidence interval [CI] 1.47-138.27) as well as the consumption of 'sprouts' (OR 10.6, 95% CI 1.16-97.59) was found. Principal places of consumption of 'salads' and 'sprouts' in outbreak cases were restaurants in southern Germany (80.0%, 95% CI 56.3%-94.3%). Microbiological analysis in Germany identified S. Bovismorbificans on sprouts, and genotype analysis confirmed that Swiss and German cases shared the same outbreak strain. The contaminated products were removed from the market in Germany, preventing an on-going outbreak., Conclusion: The combination of the applied methods and the collaboration between the two countries proved to be crucial elements of this investigation. A series of sprouts-associated salmonellosis outbreaks underpin the importance of this vegetable as a potential food-borne pathogen carrier.