Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing.

Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread of SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify and sequence the receptor binding domain (RBD) of SARS-COV-2 to characterize viral lineages present in sewersheds. Over the course of 2021, we reproducibly detected multiple SARS-COV-2 RBD lineages that have never been observed in patient samples in 9 sewersheds located in 3 states in the USA. These cryptic lineages contained between 4 to 24 amino acid substitutions in the RBD and were observed intermittently in the sewersheds in which they were found for as long as 14 months. Many of the amino acid substitutions in these lineages occurred at residues also mutated in the Omicron variant of concern (VOC), often with the same substitutions. One of the sewersheds contained a lineage that appeared to be derived from the Alpha VOC, but the majority of the lineages appeared to be derived from pre-VOC SARS-COV-2 lineages. Specifically, several of the cryptic lineages from New York City appeared to be derived from a common ancestor that most likely diverged in early 2020. While the source of these cryptic lineages has not been resolved, it seems increasingly likely that they were derived from long-term patient infections or animal reservoirs. Our findings demonstrate that SARS-COV-2 genetic diversity is greater than what is commonly observed through routine SARS-CoV-2 surveillance. Wastewater sampling may more fully capture SARS-CoV-2 genetic diversity than patient sampling and could reveal new VOCs before they emerge in the wider human population.

Genetic Diversity and Evolutionary Convergence of Cryptic SARS-CoV-2 Lineages Detected Via Wastewater Sequencing.

Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread of SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify and sequence the receptor binding domain (RBD) of SARS-COV-2 to characterize viral lineages present in sewersheds. Over the course of 2021, we reproducibly detected multiple SARS-COV-2 RBD lineages that have never been observed in patient samples in 9 sewersheds located in 3 states in the USA. These cryptic lineages contained between 4 to 24 amino acid substitutions in the RBD and were observed intermittently in the sewersheds in which they were found for as long as 14 months. Many of the amino acid substitutions in these lineages occurred at residues also mutated in the Omicron variant of concern (VOC), often with the same substitution. One of the sewersheds contained a lineage that appeared to be derived from the Alpha VOC, but the majority of the lineages appeared to be derived from pre-VOC SARS-COV-2 lineages. Specifically, several of the cryptic lineages from New York City appeared to be derived from a common ancestor that most likely diverged in early 2020. While the source of these cryptic lineages has not been resolved, it seems increasingly likely that they were derived from immunocompromised patients or animal reservoirs. Our findings demonstrate that SARS-COV-2 genetic diversity is greater than what is commonly observed through routine SARS-CoV-2 surveillance. Wastewater sampling may more fully capture SARS-CoV-2 genetic diversity than patient sampling and could reveal new VOCs before they emerge in the wider human population. Author Summary: During the COVID-19 pandemic, wastewater-based epidemiology has become an effective public health tool. Because many infected individuals shed SARS-CoV-2 in feces, wastewater has been monitored to reveal infection trends in the sewersheds from which the samples were derived. Here we report novel SARS-CoV-2 lineages in wastewater samples obtained from 3 different states in the USA. These lineages appeared in specific sewersheds intermittently over periods of up to 14 months, but generally have not been detected beyond the sewersheds in which they were initially found. Many of these lineages may have diverged in early 2020. Although these lineages share considerable overlap with each other, they have never been observed in patients anywhere in the world. While the wastewater lineages have similarities with lineages observed in long-term infections of immunocompromised patients, animal reservoirs cannot be ruled out as a potential source.

Removal and sequestration of iodide using silver-impregnated activated carbon.

Two silver-impregnated activated carbons (SIACs) (0.05 and 1.05 wt % silver) and their virgin (i.e., unimpregnated) granular activated carbon (GAC) precursors were investigated for their ability to remove and sequester iodide from aqueous solutions in a series of batch sorption and leaching experiments. Silver content, total iodide concentration, and pH were the factors controlling the removal mechanisms of iodide. Iodide uptake increased with decreasing pH for both SIACs and their virgin GACs. The 0.05% SIAC behaved similarly to its virgin GAC in all experimental conditions because of its low silver content. At pH values of 7 and 8 there was a marked increased in iodide removal for the 1.05% SIAC over that of its virgin GAC, while their performances were similar at a pH of 5. Scanning electron microscopy (SEM) and energy-dispersive X-ray (EDX) analyses prior to reaction with iodide showed the presence of metallic silver agglomerates on the 1.05% SIAC surface. After the reaction, elemental mapping with EDX showed the formation of silver iodide agglomerates. Oxidation of metallic silver was observed in the presence of oxygen, and the carbon surface appears to catalyze this reaction. When the molar ratio of silver to iodide was greater than 1 (i.e., M(Ag,SIAC) > M(I,TOTAL)), precipitation of silver iodide was the dominant removal mechanism. However, unreacted silver leached into solution with decreasing pH while iodide leaching did not occur. When M(Ag,SIAC) < M(I,TOTAL), silver iodide precipitation occurred until all available silver had reacted, and additional iodide was removed from solution by pH-dependent adsorption to the GAC. Under this condition, silver leaching did not occur while iodide leaching increased with increasing pH.