Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes

BACKGROUND

Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic regions, have led to insights into microbial diversity and the discovery of novel organisms. However, the variable nature of discriminatory regions can also act as a double-edged sword, as the sought-after variability can make it difficult to design primers for their amplification through PCR. Moreover, the most variable regions are not necessarily the most informative regions for the purpose of differentiation; one should focus on regions that maximize the number of lineages that can be distinguished.

RESULTS

Here we present AmpliDiff, a computational tool that simultaneously finds highly discriminatory genomic regions in viral genomes of a single species, as well as primers allowing for the amplification of these regions. We show that regions and primers found by AmpliDiff can be used to accurately estimate relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data. We obtain errors that are comparable with using whole genome information to estimate relative abundances. Furthermore, our results show that AmpliDiff is robust against incomplete input data and that primers designed by AmpliDiff also bind to genomes sampled months after the primers were selected.

CONCLUSIONS

With AmpliDiff we provide an effective, cost-efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.

A methodology for optimal placement of sensors in enclosed environments: A dynamical systems approach

Air quality has been an important issue in public health for many years. Sensing the level and distributions of impurities help in the control of building systems and mitigate long term health risks. Rapid detection of infectious diseases in large public areas like airports and train stations may help limit exposure and aid in reducing the spread of the disease. Complete coverage by sensors to account for any release scenario of chemical or biological warfare agents may provide the opportunity to develop isolation and evacuation plans that mitigate the impact of the attack. All these scenarios involve strategic placement of sensors to promptly detect and rapidly respond. This paper presents a data driven sensor placement algorithm based on a dynamical systems approach. The approach utilizes the finite dimensional Perron-Frobenius (PF) concept. The PF operator (or the Markov matrix) is used to construct an observability gramian that naturally incorporates sensor accuracy, location constraints, and sensing constraints. The algorithm determines the response times, sensor coverage maps, and the number of sensors needed. The utility of the procedure is illustrated using four examples: a literature example of the flow field inside an aircraft cabin and three air flow fields in different geometries. The effect of the constraints on the response times for different sensor placement scenarios is investigated. Knowledge of the response time and coverage of the multiple sensors aides in the design of mechanical systems and response mechanisms. The methodology provides a simple process for place sensors in a building, analyze the sensor coverage maps and response time necessary during extreme events, as well as evaluate indoor air quality. The theory established in this paper also allows for future work in topics related to construction of classical estimator problems for the sensors, real-time contaminant transport, and development of agent dispersion, contaminant isolation/removal, and evacuation strategies.