Yes it is always possible that an an undetected hidden piece of malware
such as a rootkit
may be present but again, there are usually symptoms of such an infection to indicate something is wrong.
Many anti-virus programs utilize optional heuristic scanning engine
features to detect brand new viruses and other types of malware, based on behaviors and coding patterns that infections commonly use. Heuristic analysis
is the ability of an anti-virus program to detect possible new variants of malware
before the vendor can get samples and update the program's definitions for detection. Heuristics uses non-specific detection methods to find new or unknown malware which allows the anti-virus to detect and stop if before doing any harm to your system. Heuristic scanning methods vary depending on the vendor. Some claim to allow emulation of the file's activities in a virtual sandbox. Others scan the file more intensively, searching line by line inspecting the code in a file to see if it contains virus-like characteristics. If the number of these characteristics/instructions exceeds a pre-defined threshold, the file is flagged as a possible virus
.Eset: Heuristic AnalysisDetecting Unknown VirusesKaspersky: What is heuristic analysis