This study provides a detailed virological analysis of nine hospitalized patients with COVID-19, focusing on virus replication, immunity, and infectivity. The findings indicate that active virus replication occurs in the upper respiratory tract, particularly in the throat, during the early stages of symptoms. Pharyngeal virus shedding was high during the first week, peaking at 7.1 × 10^6 RNA copies per throat swab on day 4. Infectious virus was isolated from throat and lung samples but not from stool or blood and urine samples. The presence of viral replicative RNA intermediates in throat samples confirmed active replication. Sequence analysis revealed distinct virus populations in throat and lung samples from one patient, supporting independent replication. Serocconversion occurred in 50% of patients by day 7 and in all by day 14, but did not lead to a rapid decline in viral load. The study highlights the importance of considering the upper respiratory tract as a site of active virus replication, which has implications for the containment of COVID-19. The findings also suggest that the transmission dynamics of SARS-CoV-2 may be more efficient than SARS due to active pharyngeal viral shedding during the mild early stages of infection.This study provides a detailed virological analysis of nine hospitalized patients with COVID-19, focusing on virus replication, immunity, and infectivity. The findings indicate that active virus replication occurs in the upper respiratory tract, particularly in the throat, during the early stages of symptoms. Pharyngeal virus shedding was high during the first week, peaking at 7.1 × 10^6 RNA copies per throat swab on day 4. Infectious virus was isolated from throat and lung samples but not from stool or blood and urine samples. The presence of viral replicative RNA intermediates in throat samples confirmed active replication. Sequence analysis revealed distinct virus populations in throat and lung samples from one patient, supporting independent replication. Serocconversion occurred in 50% of patients by day 7 and in all by day 14, but did not lead to a rapid decline in viral load. The study highlights the importance of considering the upper respiratory tract as a site of active virus replication, which has implications for the containment of COVID-19. The findings also suggest that the transmission dynamics of SARS-CoV-2 may be more efficient than SARS due to active pharyngeal viral shedding during the mild early stages of infection.