BackgroundIn March 2022, the Omicron variant of SARS-CoV-2 spread rapidly in Shanghai, China. The city adopted strict non-pharmacological intervention (NPI) measures, including lockdown (implemented on March 28 in Pudong and April 1 in Puxi) and blanket PCR testing (April 4). This study aims to understand the effect of these measures.MethodsWe tabulated daily case counts from official reports and fitted a two-patch stochastic SEIR model to the data for the period of March 19 to April 21. This model considered two regions in Shanghai, namely Pudong and Puxi, as the implementation of control measures in Shanghai was carried out on different dates in these regions. We verified our fitting results using the data from April 22 to June 26. Finally, we applied the point estimate of parameter values to simulate our model while varying the dates of control measure implementation, and studied the effectiveness of the control measures.ResultsOur point estimate for the parameter values yields expected case counts that agree well the data for both the periods from March 19 to April 21 and from April 22 to June 26. Lockdown did not significantly reduce the intra-region transmission rates. Only about 21% cases were reported. The underlying basic reproduction numberR0was 1.7, and the control reproduction number with both lockdown and blanket PCR testing was 1.3. If both measures were implemented on March 19, only about 5.9% infections would be prevented.ConclusionsThrough our analysis, we found that NPI measures implemented in Shanghai were not sufficient to reduce the reproduction number to below unity. Thus, earlier intervention only has limited effect on reducing cases. The outbreak dies out because of only 27% of the population were active in disease transmission, possibly due to a combination of vaccination and lockdown.