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Controlling the COVID-19 pandemic is an urgent global challenge. The rapid geographic spread of SARS-CoV-2 directly reflects the social structure. Before effective vaccines and treatments are widely available, we have to rely on…

SARS-CoV-2 lineages are defined according to placement in a phylogenetic tree, but approximated by a list of mutations based on sequences collected from clinical sampling. Wastewater lineage abundance is generally found under the assumption…

Mechanistic models fit to streaming surveillance data are critical to understanding the transmission dynamics of an outbreak as it unfolds in real-time. However, transmission model parameter estimation can be imprecise, and sometimes even…

Given the urgent informational needs connected with the diffusion of infection with regard to the COVID-19 pandemic, in this paper, we propose a sampling design for building a continuous-time surveillance system. Compared with other…

Background: Rapid testing for an infection is paramount during a pandemic to prevent continued viral spread and excess morbidity and mortality. This study aimed to determine whether alternative testing strategies based on sample pooling can…

The epidemiology of pandemics is classically viewed using geographical and political borders; however, these artificial divisions can result in a misunderstanding of the current epidemiological state within a given region. To improve upon…

Viral signal in wastewater offers a promising opportunity to assess and predict the burden of infectious diseases. That has driven the widespread adoption and development of wastewater monitoring tools by public health organizations. Recent…

Wastewater-based epidemiology (WBE) is an effective tool for tracking community circulation of respiratory viruses. We address estimating the effective reproduction number ($R_t$) and the relative number of infections from wastewater viral…

We propose a compressed sensing-based testing approach with a practical measurement design and a tuning-free and noise-robust algorithm for detecting infected persons. Compressed sensing results can be used to provably detect a small number…

As COVID-19 transitions into an endemic disease that remains constantly present in the population at a stable level, monitoring its prevalence without invasive measures becomes increasingly important. In this paper, we present a deep neural…

Concentrations of pathogen genomes measured in wastewater have recently become available as a new data source to use when modeling the spread of infectious diseases. One promising use for this data source is inference of the effective…

This paper deals with a clustering algorithm for histogram data based on a Self-Organizing Map (SOM) learning. It combines a dimension reduction by SOM and the clustering of the data in a reduced space. Related to the kind of data, a…

During the SARS-CoV-2 pandemic, polymerase chain reaction (PCR) and lateral flow device (LFD) tests were frequently deployed to detect the presence of SARS-CoV-2. Many of these tests were singleplex, and only tested for the presence of a…

The widely used gene quantisation technique, Lateral Flow Device (LFD), is now commonly used to detect the presence of SARS-CoV-2. It is enabling the control and prevention of the spread of the virus. Depending on the viral load, LFD have…

The outburst of COVID-19 in late 2019 was the start of a health crisis that shook the world and took millions of lives in the ensuing years. Many governments and health officials failed to arrest the rapid circulation of infection in their…

Through the use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases. We first analyse each dataset in…

There are many sources of data giving information about the number of SARS-CoV-2 infections in the population, but all have major drawbacks, including biases and delayed reporting. For example, the number of confirmed cases largely…

The SARS-CoV-2 pandemic has added new urgency to the study of viral mechanisms of infection. But while vaccines offer a measure of protection against this specific outbreak, a new era of pandemics has been predicted. In addition to this,…

This paper presents a critical analysis of the literature and perspective research ideas for modeling the epidemics caused by the SARS-CoV-2 virus. It goes beyond deterministic population dynamics to consider several key complexity features…

In the present paper, we model the cumulative number of persons reported to be infected by the SARS-CoV-2 virus, in a country or a region, by a sum of logistic functions. For a given logistic function, using Eulerian numbers, we find the…