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

BackgroundRecently, more patients who 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 controvers...

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Autores principales:	Yingping Wu, Shufa Zheng, Tian Liu, Xueke Liu, Huina Tang, Yutong He, Wei Xu, Lele Li, Wenxu Yu, Ke Xing, Xiaoping Xia
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	SARS-CoV-2 whole-genome sequencing viral haplotype COVID-19 prolonged viral shedding Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/0810d155e6f24716af69574836f42a05
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spelling	oai:doaj.org-article:0810d155e6f24716af69574836f42a052021-11-09T15:33:28ZViral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding2235-298810.3389/fcimb.2021.715143https://doaj.org/article/0810d155e6f24716af69574836f42a052021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fcimb.2021.715143/fullhttps://doaj.org/toc/2235-2988BackgroundRecently, more patients who 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 for clinical cases of long-term viral shedding, it remains unclear whether the persistent viral shedding means re-infection or recurrence.MethodsSpecimens were collected from three COVID-19-confirmed patients, and whole-genome sequencing was performed on these clinical specimens during their first hospital admission with a high viral load of SARS-CoV-2. Laboratory tests were examined and analyzed throughout the whole course of the disease. Phylogenetic analysis was carried out for SARS-CoV-2 haplotypes.ResultsWe 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), which was verified as one kind of viral haplotype. Patients YW01 and YW02 were admitted to the hospital after being infected with COVID-19 as members of a family cluster, 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.ConclusionThese findings show 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. However, the correlation between haplotype diversity of SARS-CoV-2 virus and immune status is not absolute. It showed important implications for the clinical management strategies for COVID-19 patients with long-term hospitalization or cases of recurrence.Yingping WuShufa ZhengTian LiuXueke LiuHuina TangYutong HeWei XuLele LiWenxu YuKe XingXiaoping XiaFrontiers Media S.A.articleSARS-CoV-2whole-genome sequencingviral haplotypeCOVID-19prolonged viral sheddingMicrobiologyQR1-502ENFrontiers in Cellular and Infection Microbiology, Vol 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	SARS-CoV-2 whole-genome sequencing viral haplotype COVID-19 prolonged viral shedding Microbiology QR1-502
spellingShingle	SARS-CoV-2 whole-genome sequencing viral haplotype COVID-19 prolonged viral shedding Microbiology QR1-502 Yingping Wu Shufa Zheng Tian Liu Xueke Liu Huina Tang Yutong He Wei Xu Lele Li Wenxu Yu Ke Xing Xiaoping Xia Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding
description	BackgroundRecently, more patients who 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 for clinical cases of long-term viral shedding, it remains unclear whether the persistent viral shedding means re-infection or recurrence.MethodsSpecimens were collected from three COVID-19-confirmed patients, and whole-genome sequencing was performed on these clinical specimens during their first hospital admission with a high viral load of SARS-CoV-2. Laboratory tests were examined and analyzed throughout the whole course of the disease. Phylogenetic analysis was carried out for SARS-CoV-2 haplotypes.ResultsWe 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), which was verified as one kind of viral haplotype. Patients YW01 and YW02 were admitted to the hospital after being infected with COVID-19 as members of a family cluster, 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.ConclusionThese findings show 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. However, the correlation between haplotype diversity of SARS-CoV-2 virus and immune status is not absolute. It showed important implications for the clinical management strategies for COVID-19 patients with long-term hospitalization or cases of recurrence.
format	article
author	Yingping Wu Shufa Zheng Tian Liu Xueke Liu Huina Tang Yutong He Wei Xu Lele Li Wenxu Yu Ke Xing Xiaoping Xia
author_facet	Yingping Wu Shufa Zheng Tian Liu Xueke Liu Huina Tang Yutong He Wei Xu Lele Li Wenxu Yu Ke Xing Xiaoping Xia
author_sort	Yingping Wu
title	Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding
title_short	Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding
title_full	Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding
title_fullStr	Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding
title_full_unstemmed	Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding
title_sort	viral haplotypes in covid-19 patients associated with prolonged viral shedding
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/0810d155e6f24716af69574836f42a05
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Viral Haplotypes in COVID-19 Patients Associated With Prolonged Viral Shedding

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