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Heating, ventilation and air-conditioning (HVAC) system is favourable for regulating indoor temperature, relative humidity, airflow pattern and air quality. However, HVAC systems may turn out to be the culprit of microbial contamination in enclosed spaces and deteriorate the environment due to inappropriate design and operation. In the context of COVID-19, significant transformations and new requirements are occurring in HVAC systems. Recently, several updated operational guidelines for HVAC systems have been issued by various institutions to control the airborne transmission and mitigate infection risks in enclosed environments. Challenges and innovations emerge in response to operational variations of HVAC systems. To efficiently prevent the spread of the pandemic and reduce infection risks, it is essential to have an overall understanding of impacts caused by COVID-19 on HVAC systems. Therefore, the objectives of this article are to: (a) provide a comprehensive review of the airborne transmission characteristics of SARS-CoV-2 in enclosed spaces and a theoretical basis for HVAC operation guideline revision; (b) investigate HVAC-related guidelines to clarify the operational variations of HVAC systems during the pandemic; (c) analyse how operational variations of HVAC systems affect energy consumption; and (d) identify the innovations and research trends concerning future HVAC systems. Furthermore, this paper compares the energy consumption of HVAC system operation during the normal times versus pandemic period, based on a case study in China, providing a reference for other countries around the world. Results of this paper offer comprehensive insights into how to keep indoor environments safe while maintaining energy-efficient operation of HVAC systems.