Metagenomic Next-Generation Sequencing Reveals the Profile of Viral Infections in Kidney Transplant Recipients During the COVID-19 Pandemic

• DOI: 10.3389/fpubh.2022.888064
• Publication Date: 2022-07-11T05:44:27Z
• Authors: Xiangyong Tian; Wenjing Duan; Xiulei Zhang; Xiaoqiang Wu; Chan Zhang; Zhiwei Wang; Guanghui Cao; Yue Gu; Fengmin Shao; Tianzhong Yan
• Keywords: Torque teno virus; 0301 basic medicine; torque teno virus; kidney transplantation; COVID-19; High-Throughput Nucleotide Sequencing; virus; Kidney Transplantation; metagenomic next-generation sequencing; infection; 6. Clean water; 3. Good health; 03 medical and health sciences; Virus Diseases; Cytomegalovirus Infections; DNA, Viral; Animals; Humans; Public Health; Public aspects of medicine; RA1-1270; Pandemics

BackgroundTo study the clinical application of metagenomic next-generation sequencing (mNGS) in the detection of viral infections in kidney transplant recipients (KTRs) during the COVID-19 pandemic.MethodsUsing mNGS technology, 50 human fluid samples of KTRs were detected, including 20 bronchoalveolar lavage fluid (BALF) samples, 21 urine samples and 9 blood samples. The detected nucleic acid sequences were compared and analyzed with the existing viral nucleic acid sequences in the database, and the virus infection spectrum of KTRs was drawn.ResultsThe viral nucleic acids of 15 types of viruses were detected in 96.00% (48/50) of the samples, of which 11 types of viruses were in BALF (95.00%, 19/20), and the dominant viruses were torque teno virus (TTV) (65.00%; 13/20), cytomegalovirus (CMV) (45.00%; 9/20) and human alphaherpesvirus 1 (25.00%; 5/20). 12 viruses (95.24%, 20/21) were detected in the urine, and the dominant viruses were TTV (52.38%; 11/21), JC polyomavirus (52.38%; 11/21), BK polyomavirus (42.86%; 9/21), CMV (33.33%; 7/21) and human betaherpesvirus 6B (28.57%; 6/21). 7 viruses were detected in the blood (100.00%, 9/9), and the dominant virus was TTV (100.00%; 9/9). Four rare viruses were detected in BALF and urine, including WU polyomavirus, primate bocaparvovirus 1, simian virus 12, and volepox virus. Further analysis showed that TTV infection with high reads indicated a higher risk of acute rejection (P < 0.05).ConclusionsmNGS detection reveals the rich virus spectrum of infected KTRs, and improves the detection rate of rare viruses. TTV may be a new biomarker for predicting rejection.