Abstract Background The disease burden of SARS-CoV-2 as measured by tests from various localities, and at different time points present varying estimates of infection and fatality rates. Models based on these acquired data may suffer from systematic errors and large estimation variances due to the biases associated with testing. An unbiased randomized testing to estimate the true fatality rate is still missing. Methods Here, we characterize the effect of incidental sampling bias in the estimation of epidemic dynamics. Towards this, we explicitly modeled for sampling bias in an augmented compartment model to predict epidemic dynamics. We further calculate the bias from differences in disease prediction from biased, and randomized sampling, proposing a strategy to obtain unbiased estimates. Results Our simulations demonstrate that sampling biases in favor of patients with higher disease manifestation could significantly affect direct estimates of infection and fatality rates calculated from the numbers of confirmed cases and deaths, and serological testing can partially mitigate these biased estimates. Conclusions The augmented compartmental model allows the explicit modeling of different testing policies and their effects on disease estimates. Our calculations for the dependence of expected confidence on a randomized sample sizes, show that relatively small sample sizes can provide statistically significant estimates for SARS-CoV-2 related death rates.