Effect of risk status for severe COVID-19 on individual contact behaviour during the SARS-CoV-2 pandemic in 2020/2021-an analysis based on the German COVIMOD study.

BACKGROUND: One of the primary aims of contact restriction measures during the SARS-CoV-2 pandemic has been to protect people at increased risk of severe disease from the virus. Knowledge about the uptake of contact restriction measures in this group is critical for public health decision-making. We analysed data from the German contact survey COVIMOD to assess differences in contact patterns based on risk status, and compared this to pre-pandemic data to establish whether there was a differential response to contact reduction measures. METHODS: We quantified differences in contact patterns according to risk status by fitting a generalised linear model accounting for within-participant clustering to contact data from 31 COVIMOD survey waves (April 2020-December 2021), and estimated the population-averaged ratio of mean contacts of persons with high risk for a severe COVID-19 outcome due to age or underlying health conditions, to those without. We then compared the results to pre-pandemic data from the contact surveys HaBIDS and POLYMOD. RESULTS: Averaged across all analysed waves, COVIMOD participants reported a mean of 3.21 (95% confidence interval (95%CI) 3.14,3.28) daily contacts (truncated at 100), compared to 18.10 (95%CI 17.12,19.06) in POLYMOD and 28.27 (95%CI 26.49,30.15) in HaBIDS. After adjusting for confounders, COVIMOD participants aged 65 or above had 0.83 times (95%CI 0.79,0.87) the number of contacts as younger age groups. In POLYMOD, this ratio was 0.36 (95%CI 0.30,0.43). There was no clear difference in contact patterns due to increased risk from underlying health conditions in either HaBIDS or COVIMOD. We also found that persons in COVIMOD at high risk due to old age increased their non-household contacts less than those not at such risk after strict restriction measures were lifted. CONCLUSIONS: Over the course of the SARS-CoV-2 pandemic, there was a general reduction in contact numbers in the German population and also a differential response to contact restriction measures based on risk status for severe COVID-19. This differential response needs to be taken into account for parametrisations of mathematical models in a pandemic setting.

Individual social contact data and population mobility data as early markers of SARS-CoV-2 transmission dynamics during the first wave in Germany-an analysis based on the COVIMOD study.

BACKGROUND: The effect of contact reduction measures on infectious disease transmission can only be assessed indirectly and with considerable delay. However, individual social contact data and population mobility data can offer near real-time proxy information. The aim of this study is to compare social contact data and population mobility data with respect to their ability to reflect transmission dynamics during the first wave of the SARS-CoV-2 pandemic in Germany. METHODS: We quantified the change in social contact patterns derived from self-reported contact survey data collected by the German COVIMOD study from 04/2020 to 06/2020 (compared to the pre-pandemic period from previous studies) and estimated the percentage mean reduction over time. We compared these results as well as the percentage mean reduction in population mobility data (corrected for pre-pandemic mobility) with and without the introduction of scaling factors and specific weights for different types of contacts and mobility to the relative reduction in transmission dynamics measured by changes in R values provided by the German Public Health Institute. RESULTS: We observed the largest reduction in social contacts (90%, compared to pre-pandemic data) in late April corresponding to the strictest contact reduction measures. Thereafter, the reduction in contacts dropped continuously to a minimum of 73% in late June. Relative reduction of infection dynamics derived from contact survey data underestimated the one based on reported R values in the time of strictest contact reduction measures but reflected it well thereafter. Relative reduction of infection dynamics derived from mobility data overestimated the one based on reported R values considerably throughout the study. After the introduction of a scaling factor, specific weights for different types of contacts and mobility reduced the mean absolute percentage error considerably; in all analyses, estimates based on contact data reflected measured R values better than those based on mobility. CONCLUSIONS: Contact survey data reflected infection dynamics better than population mobility data, indicating that both data sources cover different dimensions of infection dynamics. The use of contact type-specific weights reduced the mean absolute percentage errors to less than 1%. Measuring the changes in mobility alone is not sufficient for understanding the changes in transmission dynamics triggered by public health measures.

Data Analysis Strategies for Microbiome Studies in Human Populations-a Systematic Review of Current Practice.

Reproducibility is a major issue in microbiome studies, which is partly caused by missing consensus about data analysis strategies. The complex nature of microbiome data, which are high-dimensional, zero-inflated, and compositional, makes them challenging to analyze, as they often violate assumptions of classic statistical methods. With advances in human microbiome research, research questions and study designs increase in complexity so that more sophisticated data analysis concepts are applied. To improve current practice of the analysis of microbiome studies, it is important to understand what kind of research questions are asked and which tools are used to answer these questions. We conducted a systematic literature review considering all publications focusing on the analysis of human microbiome data from June 2018 to June 2019. Of 1,444 studies screened, 419 fulfilled the inclusion criteria. Information about research questions, study designs, and analysis strategies were extracted. The results confirmed the expected shift to more advanced research questions, as one-third of the studies analyzed clustered data. Although heterogeneity in the methods used was found at any stage of the analysis process, it was largest for differential abundance testing. Especially if the underlying data structure was clustered, we identified a lack of use of methods that appropriately addressed the underlying data structure while taking into account additional dependencies in the data. Our results confirm considerable heterogeneity in analysis strategies among microbiome studies; increasingly complex research questions require better guidance for analysis strategies.IMPORTANCE The human microbiome has emerged as an important factor in the development of health and disease. Growing interest in this topic has led to an increasing number of studies investigating the human microbiome using high-throughput sequencing methods. However, the development of suitable analytical methods for analyzing microbiome data has not kept pace with the rapid progression in the field. It is crucial to understand current practice to identify the scope for development. Our results highlight the need for an extensive evaluation of the strengths and shortcomings of existing methods in order to guide the choice of proper analysis strategies. We have identified where new methods could be designed to address more advanced research questions while taking into account the complex structure of the data.