Dear Mr. Zemenu Tadesse , If I get your question right what you wanted to study is the burden of infectious disease/s at health facilities. This will be a simple institution based cross-sectional study. I think the timing of the study which is before or after the COVID-19 will not affect the study design.
A cross sectional multi disciplinary study would be ideal focusing on all parameters and problematic and causative factors involved with communicable diseases.
Given the possible lack of resources, one way to assess disease prevalence is by using a random number table, rather than trying to study everyone. When patients register in the clinic, you can select a number to study based on your view of how many people would be representative of the community at large. The time interval could be a week or other time frame suitable to your situation. This strategy was used successfully in Lesotho regarding HIV seroprevalence.
Dear zemenu, if your primary objective is to assess the prevalence of communicable disease at health institution level...you should use institution based cross sectional study design.
Your probable outcome should be in the title....If you want to compare or just a local survey among the institutes about disease burden clear it first.