In most of the research paper people used both neutral and alkaline comet assay to determine the level of DNA damage either single stranded or double stranded but the exact principle of both the methods are undetermined.
Somya Ranjan Dash The neutral comet assay allows the detection of double-strand breaks, where alkaline comet assay detects single-strand breaks. Go through the below mentioned article. It might help you.
Article Mechanisms of DNA exit during neutral and alkaline comet assay
The alkaline comet assay method allows for analysis of global dna damage (Single strand breaks + double strand breaks) in your samples (cells). This allows much more sensitivity for detecting smaller amounts of DNA damage, including single and double strand DNA breaks, alkali-labile sites, DNA-DNA / DNA-protein cross-linking, and DNA single-strand breaks associated with incomplete excision repair sites.