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ObjectiveTo investigate the quality of disinfection in the SARS-CoV-2 nucleic acid sampling sites in Shanghai.MethodsSwab samples of medical staff’ hands and environments of different SARS-CoV-2 nucleic acid sampling sites were collected from July to September 2022， with the total number of bacterial colonies cultured and counted.ResultsA total of 728 swab samples were collected from 69 sampling sites. The median total number of bacterial colonies on hand surface， object surface and air samples were 0 CFU·cm-2， 0 CFU·cm-2， and 1 CFU·（petri dish∙5 min）-1， respectively， and P95 was 13 CFU·cm-2， 5.3 CFU·cm-2， and 17.8 CFU·（culture vessel∙5 min）-1， respectively. According to the GB 15982‒2012 Hygienic Standard for Disinfection in Hospitals class Ⅳ environment， 680 samples met the standard （93.4%）. Furthermore， 96.9%， 92.0%， and 92.2% of the samples in the sampling sites of tertiary/secondary hospitals， community health centers， and community convenience sampling sites met the standard， respectively. Quality of disinfection did not differ significantly across these sampling sites.ConclusionThe quality of disinfection in the SARS-CoV-2 nucleic acid sampling sites in Shanghai is generally good. Additionally， hand hygiene of medical staff and disinfection on object surface in some sampling sites need to be strengthened.