Search

The emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) was met with rapid development of robust molecular-based detection assays. Many SARS-CoV-2 molecular tests target multiple genetic regions of the virus to maximize detection and protect against diagnostic escape. Despite the relatively moderate mutational rate of SARS-CoV-2, numerous mutations with known negative impact on diagnostic assays have been identified. In early 2021, we identified four samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing revealed a single common mutation in the N gene C29200T. Spatiotemporal analysis showed that the mutation was found in at least six different Canadian provinces from May 2020 until May 2021. Phylogenetic analysis showed that this mutation arose multiple times in Canadian samples and is present in six different variants of interest and of concern. The Cepheid testing platform is commonly used in Canada including in remote regions. As such, the existence of N gene mutation dropouts required further investigation. While commercial SARS-CoV-2 molecular detection assays have contributed immensely to the response effort, many vendors are reluctant to make primer/probe sequences publicly available. Proprietary primer/probe sequences create diagnostic 'blind spots' for global SARS-CoV-2 sequence monitoring and limits the ability to detect and track the presence and prevalence of diagnostic escape mutations. We hope that our industry partners will seriously consider making primer/probe sequences available, so that diagnostic escape mutants can be identified promptly and responded to appropriately to maintain diagnostic accuracy. [ABSTRACT FROM AUTHOR]

We used 4 years of publicly available data (2016–2019) on chemical usage at salmon sites with information on production, stocking, locations and environmental conditions to explore patterns of anti-sea lice treatments in a Canadian province. Results show that sequential chemical treatments are prevalent, emamectin benzoate (EMB) with azamethiphos being the most used combination with a decrease in ivermectin usage. Relatively high rates of usage of EMB per fish biomass may point to potential lice resistance patterns with information needed on mechanisms and local populations. Lower or no chemical usage at some sites indicate less sea lice infestations likely influenced by localized site conditions (coves), and a lessened need for medication due to the usage of cleaner fish and possibly other non-chemical methods (not documented in this report). The year/climate influenced chemical input only in sites with higher treatment levels likely due to effects on sea lice growth and reproduction. Observed differences between years are warmer surface temperature in the fall, a higher freshwater input in spring, and stronger wind conditions for 2017 and 2018 with more medication usage for these two years. The lack of significant effect of site distances calculated in zones of influence based on 24 h potential connectivity patterns highlight the need to refine the resolution of hydrodynamic processes. [ABSTRACT FROM AUTHOR]

White chanterelles (Basidiomycota), lacking the orange pigments and apricot-like odour of typical chanterelles, were found recently in the Canadian provinces of Québec (QC) and Newfoundland & Labrador (NL). Our phylogenetic analyses confirmed the identification of all white chanterelles from NL and QC as Cantharellus enelensis; we name these forma acolodorus. We characterized carotenoid pigments, lipids, phenolics, and volatile compounds in these and related chanterelles. White mutants of C. enelensis lacked detectable β-carotene, confirmed to be the primary pigment of wild-type, golden-orange individuals, and could also be distinguished by their profiles of fatty acids and phenolic acids, and by the ketone and terpene composition of their volatiles. We detected single base substitutions in the phytoene desaturase (Al-1) and phytoene synthase (Al-2) genes of the white mutant, which are predicted to result in altered amino acids in their gene products and may be responsible for the loss of β-carotene synthesis in that form. [ABSTRACT FROM AUTHOR]