Leveraging wastewater surveillance to actively monitor Covid-19 community dynamics in rural areas with reduced reliance on clinical testing (preprint)

The prevalence of COVID-19 in the community has become more difficult to gauge utilizing clinical testing due to a decrease in reported test results stemming from the availability of at-home test kits and a reduction in the number of cases seeking medical treatment. The purpose of this study was to examine the trend of diminishing correlation between reported clinical cases of COVID-19 and wastewater-based surveillance epidemiological data as home testing became available in the Eastern Upper Peninsula of Michigan. Wastewater grab samples were collected weekly from 16 regional locations from June 2021-December 2022. Samples were analyzed for SARS-CoV-2 N1 and N2 viral particles using reverse transcriptase digital droplet polymerase chain reaction (RT ddPCR). N1 and N2 gene copies were correlated with clinical cases. The t-test was used to determine correlation deterioration point. Clinical cases post-deterioration were calculated for high-correlated pre-deterioration locations using linear regression. Correlation between the wastewater-based surveillance of SARS-CoV-2 and reported clinical cases deteriorated after February 1, 2022. This corresponds with the timeframe in which commercially available at-home test kits became available in the United States. The increase in at-home testing for SARS-CoV-2 likely contributed to the decrease in reported clinical positive tests in early 2022, providing an unrealistic picture of the presence of Covid-19 in the community. As measures to reduce exposure such as personal masking, clinical testing, social isolating, and quarantining continue to decline, wastewater surveillance for the presence of SARS-CoV-2 may be the best method for public health professionals to remain aware of virus dynamics in localized regions. Time-series modeling adds another layer of information when clinical data is unobtainable or underreported.

Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning (preprint)

SARS-CoV-2 has continued to evolve throughout the COVID-19 pandemic, giving rise to multiple variants of concern (VOCs) with different biological properties. As the pandemic progresses, it will be essential to test in near real time the potential of any new emerging variant to cause severe disease. BA.1 (Omicron) was shown to be attenuated compared to the previous VOCs like Delta, but it is possible that newly emerging variants may regain a virulent phenotype. Hamsters have been proven to be an exceedingly good model for SARS-CoV-2 pathogenesis. Here, we aimed to develop robust quantitative pipelines to assess the virulence of SARS-CoV-2 variants in hamsters. We used various approaches including RNAseq, RNA in situ hybridization, immunohistochemistry, and digital pathology, including software assisted whole section imaging and downstream automatic analyses enhanced by machine learning, to develop methods to assess and quantify virus-induced pulmonary lesions in an unbiased manner. Initially, we used Delta and Omicron to develop our experimental pipelines. We then assessed the virulence of recent Omicron sub-lineages including BA.5, XBB, BQ.1.18, BA.2 and BA.2.75. We show that in experimentally infected hamsters, accurate quantification of alveolar epithelial hyperplasia and macrophage infiltrates represent robust markers for assessing the extent of virus-induced pulmonary pathology, and hence virus virulence. In addition, using these pipelines, we could reveal how some Omicron sub-lineages (e.g., BA.2.75) have regained virulence compared to the original BA.1. Finally, to maximise the utility of the digital pathology pipelines reported in our study, we developed an online repository containing representative whole organ histopathology sections that can be visualised at variable magnifications (https://covid-atlas.cvr.gla.ac.uk). Overall, this pipeline can provide unbiased and invaluable data for rapidly assessing newly emerging variants and their potential to cause severe disease.

The short‐term economic consequences of COVID‐19: Occupation tasks and mental health in Canada

In this paper, we study the effect of COVID‐19 on the labour market and reported mental health of Canadians. To better understand the effect of the pandemic on the labour market, we build indexes for whether workers: (i) are relatively more exposed to disease, (ii) work in proximity to co‐workers, (iii) are essential workers and (iv) can easily work remotely. Our estimates suggest that the impact of COVID‐19 was significantly more severe for workers that work in proximity to co‐workers and those more exposed to disease who are not in the health sector, while the effects are less severe for essential workers and workers that can work remotely. Last, using the Canadian Perspective Survey Series, we observe that reported mental health is significantly lower among some of the most affected workers such as women and less‐educated workers. We also document that those who were absent from work because of COVID‐19 are more concerned with meeting their financial obligations and with losing their job than those who continue working outside their home.

The short-term economic consequences of COVID-19: Occupation tasks and mental health in Canada

. In this paper, we study the effect of COVID-19 on the labour market and reported mental health of Canadians. To better understand the effect of the pandemic on the labour market, we build indexes for whether workers: (i) are relatively more exposed to disease, (ii) work in proximity to co-workers, (iii) are essential workers and (iv) can easily work remotely. Our estimates suggest that the impact of COVID-19 was significantly more severe for workers that work in proximity to co-workers and those more exposed to disease who are not in the health sector, while the effects are less severe for essential workers and workers that can work remotely. Last, using the Canadian Perspective Survey Series, we observe that reported mental health is significantly lower among some of the most affected workers such as women and less-educated workers. We also document that those who were absent from work because of COVID-19 are more concerned with meeting their financial obligations and with losing their job than those who continue working outside their home. Résumé Conséquences économiques de la COVID-19 à court terme : tâches professionnelles et santé mentale au Canada. Dans cet article, nous étudions les répercussions de la COVID-19 sur le marché de l?emploi et la santé mentale déclarée des Canadiens. Afin de mieux comprendre les effets de la pandémie sur le marché du travail, nous avons développé des indices permettant de déterminer si les travailleurs : 1) sont relativement plus exposés à la maladie;2) exercent leur activité à proximité de leurs collègues;3) sont essentiels;4) peuvent facilement travailler à distance. D?après nos estimations, les conséquences de la COVID-19 se sont avérées nettement plus sévères chez les travailleurs exerçant à proximité de leurs collègues ainsi que les professionnels (hors secteur médical) davantage exposés à la maladie, mais moins importantes chez les travailleurs essentiels et les télétravailleurs. Enfin, en nous appuyant sur l?une des enquêtes sur les perspectives canadiennes, nous observons que la santé mentale déclarée est nettement inférieure chez les travailleurs les plus touchés, notamment les femmes et les travailleurs moins instruits. Nous montrons également que les personnes écartées de leur travail en raison de la COVID-19 se soucient davantage du respect de leurs obligations financières et de la perte de leur emploi par rapport à celles qui ont pu continuer à travailler hors de leur domicile.