Viral Haplotypes in COVID-19 Patients Associated with Prolonged Viral Shedding

Background: Recently, more patients recovered from the novel coronavirus disease 2019 (COVID-19) may later test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) again using reverse transcription polymerase chain reaction (RT-PCR) testing. Even though it is still controversial about the possible explanation of “re-positive” patients, it remains unclear whether the persistent viral shedding means re-infection or recurrence. Methods: Specimens were collected from three COVID-19- confirmed patients, and whole genome sequencing was performed on these clinical specimens during their first hospital admission. Laboratory tests were examined and analyzed throughout the whole course of the disease. Phylogenetic analysis was carried out for SARS-CoV-2 haplotypes. Findings: We found haplotypes of SARS-CoV-2 co-infection in two COVID-19 patients (YW01 and YW03) with a long period of hospitalization. However, only one haplotype was observed in the other patient with chronic lymphocytic leukemia (YW02), who was verified to have one kind of viral haplotype. Patient YW01 and YW02 belonged to the same family cluster infection case, but they had different haplotype characteristics in the early stage of infection; YW01 and YW03 were from different infection sources; however, similar haplotypes were found together. Interpretation: These findings showed that haplotype diversity of SARS-CoV-2 may result in viral adaptation for persistent shedding in multiple recurrences of COVID-19 patients, who met the discharge requirement, but there was no absolute correlation between haplotype diversity of SARS-CoV-2 virus and immune status. It showed important implications for the clinical management strategies for COVID-19 patients with long-term hospitalization or cases of recurrence. Funding Statement: This work was supported by grants from Zhejiang Province Public Welfare Technology Application Research Project (No. LBY21H190001 to YP Wu), Guangdong Key Project in “Development of new tools for diagnosis and treatment of Autism” (No. 2018B030335001 to K Xing), Jinhua Science and Technology Bureau (No. 2020XG- 28 to XP Xia and No. 2018-4-141 to YP Wu), and Department of the Education of Zhejiang Province (No. Y201839729 and Y202045827 to YP Wu). Declaration of Interests: All authors declare no conflict of interest. Ethics Approval Statement: This study was approved by the Ethics Committee of the Fourth Affiliated Hospital, College of Medicine, Zhejiang University (Approval No.K20200026).