SARS‐CoV‐2 whole‐proteome sequences from environment as an indicator of community viral distribution, evolution and epidemiological dynamics: A cohort analysis of Austria

Abstract

Several investigations have been carried out to detect SARS‐CoV‐2 samples from the environment such as sewage waters and surface swabs. Whole‐proteome sequence analysis of 847 SARS‐CoV‐2 genome sequences collected from the environment in Austria during 2021 and deposited in GISAID indicates that alpha and delta are two dominant variants, coinciding with the human clinical samples with a Pearson correlation coefficient in the range of 0.58 (alpha variant) to 0.82 (delta variant). Both environmental and human samples show that Austrian SARS‐CoV‐2 alpha variant is found to possess N protein R203K and G204R/P mutations, whereas they are absent in the delta variant. SARS‐CoV‐2 delta variant is continuously seen in both the environmental and human clinical samples from the month of September 2021 and it spiked in November 2021, which is directly reflected in the increase of the number of SARS‐CoV‐2 infections and deaths in Austria during November 2021. Thus, the results presented here indicate that the environmental SARS‐CoV‐2 whole‐genome sequences collected from Austria reflect the community viral distribution, evolution and the concomitant epidemiological dynamics. Since SARS‐CoV‐2 keeps evolving, the results presented here further suggest the need to monitor the environment for the early detection of SARS‐CoV‐2 variants to take appropriate precautionary measures.

CoVe-Tracker: An Interactive SARS-CoV-2 Pan Proteome Evolution Tracker

“…As discussed in our previous studies, − the variations (mutations) in the amino acid sequences such as substitutions, deletions, and insertions corresponding to a total of 26 proteins were automatically obtained in the CSV file format and used as a master file in the custom data visualization. Using this master data file, the high (percentage frequency (PF) greater than 10%), moderate (PF = 1–10%), and low (PF below 1% but occur at least three times) recurring mutations were calculated as discussed elsewhere. − Additionally, the nucleotide mutations in the entire genome of SARS-CoV-2 were collected in a master “.csv” file and utilized in data visualization. The entire analysis was carried out using an in-house Python script.…”