Broiler chickens play a vital role in global food security, particularly in meat production. The complex gastrointestinal microbiome in chickens is crucial for overall health, affecting metabolism and immunity, however, the impact of viral infections remains insufficiently studied. This study investigates the virome of 5 and 25 days old broilers from two farms, utilizing the PathoSense diagnostic tool and platform to identify and quantify viral loads using nanopore sequencing methodology. At 5 days of age, only Astrovirus was identified in both farms. In contrast, at 25 days, on Farm 1 three viruses were identified, Astrovirus, avian Orthoreovirus and infectious bronchitis virus, while on Farm 2 five viruses were revealed, Astrovirus, chicken Calicivirus, Gallivirus, Sicinivirus and infectious bronchitis virus. These findings suggest an early and intensive infection via vertical transmission and later horizontal spread and viral diversification. The compromise of the immunity at an early age could facilitate viral spread and diversification. This study highlights the necessity for enhanced biosecurity measures and targeted interventions in poultry management, from parent flocks, hatcheries to production farms, and the used simple and rapid method could be a good bioindicator for improvement of flock health and mitigation of the economic impacts of viral diseases.