Detection of phythium spp. in gold course irrigation systems

Many Pythium spp. are causal agents of disease on creeping bentgrass putting greens. Phytopathogenic Pythium spp. are known to disseminate through irrigation systems in agricultural settings, and this study provides evidence that Pythium spp. also disseminate through golf course irrigation systems. Water samples were collected from irrigation heads and water sources at ten golf courses in Missouri and Kansas. Samples were collected from 2018 to 2019 in April, July, and October. Phosphorus, nitrogen, and chloride concentrations were quantified for irrigation head samples taken each sampling month to determine if these parameters influence Pythium frequency. Pythium spp. were detected in samples through baiting and membrane filtration. Cultures were isolated on PARP media and DNA was extracted from putative Pythium isolates. ITS regions were PCR amplified, sequenced, and compared with Genbank accessions. Phylogenetic trees were constructed using representative sample sequences, sequences from seven morphologically identified reference isolates, and similar Genbank accessions. Detected species include Lagenidium giganteum, Pythium biforme, P. insidiosum, P. marsipium, P. plurisporium, and Saprolegnia hypogyna. Twenty-one clades lacked species-level resolution, and 14 of these clades were associated with Pythium species. Clades A, C, D, E, I, and M contain pathogenic Pythium species that cause root and crown rot on creeping bentgrass. Detected Pythium communities were dependent on the detection method used and sampling source. Pythium frequency and diversity were highest in April 2019. Sample temperature, sampling site, chloride, and nutrient concentrations did not influence Pythium frequency in samples. All irrigation systems that utilized surface water sources contained at least three Pythium spp. over the course of two years.Includes bibliographical references

Tracking cryptic SARS-CoV-2 Lineages Detected in NYC Wastewater

Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID’s EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir

Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater.

Deep sequencing of wastewater to detect SARS-CoV-2 has been used during the COVID-19 pandemic to monitor viral variants as they appear and circulate in communities. SARS-CoV-2 lineages of an unknown source that have not been detected in clinical samples, referred to as cryptic lineages, are sometimes repeatedly detected from specific locations. We have continued to detect one such lineage previously seen in a Missouri site. This cryptic lineage has continued to evolve, indicating continued selective pressure similar to that observed in Omicron lineages