Background A pandemic of coronavirus disease MESHD 2019 (COVID-19) caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) has been spreading over the world. However, the viral dynamics, host serologic responses, and their associations with clinical manifestations, have not been well described in prospective cohort. Methods We conducted a prospective cohort and enrolled 67 COVID-19 patients admitting between Jan 26 and Feb 5, 2020. Clinical specimens including nasopharyngeal swab, sputum, blood SERO, urine and stool were tested periodically according to standardized case report form with final follow-up on February 27. The routes and duration of viral shedding, antibody SERO response, and their associations with disease MESHD severity and clinical manifestations were systematically evaluated. Coronaviral particles in clinical specimens were observed by transmission TRANS electron microscopy (TEM). Results The median duration of SARS-CoV-2 RNA shedding were 12 (3-38), 19 (5-37), and 18 (7-26) days in nasopharyngeal swabs, sputum and stools, respectively. Only 13 urines (5.6%) and 12 plasmas SERO (5.7%) were viral positive. Prolonged viral shedding was observed in severe patients than that of non-severe patients. Cough MESHD Cough HP but not fever MESHD fever HP, aligned with viral shedding in clinical respiratory specimens, meanwhile the positive stool-RNA appeared to align with the proportion who concurrently had cough MESHD cough HP and sputum production, but not diarrhea MESHD diarrhea HP. Typical coronaviral particles could be found directly in sputum by TEM. The anti-nucleocapsid-protein IgM started on day 7 and positive rate peaked on day 28, while that of IgG was on day 10 and day 49 after illness onset. IgM and IgG appear earlier, and their titers are significantly higher in severe patients than non-severe patients (p<0.05). The weak responders for IgG had a significantly higher viral clearance rate than that of strong responders (p= 0.011). Conclusions Nasopharyngeal, sputum and stools rather than blood SERO and urine, were the major shedding routes for SARS-CoV-2, and meanwhile sputum had a prolonged viral shedding. Symptom cough MESHD cough HP seems to be aligned with viral shedding in clinical respiratory and fecal specimens. Stronger antibody SERO response was associated with delayed viral clearance and disease MESHD severity.