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An efficient method to enhance recovery and detection of SARS-CoV-2 rna in wastewater

Journal of Environmental Sciences 2023年第8期130卷 139-148页

作者： Teresa Kumblathan Yanming Liu Yuanyuan Qiu Lilly Pang Steve E.Hrudey X.Chris Le Xing-Fang Li Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada Division of Diagnostic and Applied Microbiology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonT6G 2G3Canada Public Health Laboratory Alberta Precision LaboratoriesEdmontonAlbertaT6G 2G3Canada

Wastewater surveillance(WS)of SARS-CoV-2 currently requires multiple steps and suffers low recoveries and poor sensitivity.Here,we report an improved analytical method with high sensitivity and recovery to quantify SARS-CoV-2 rna in wastewater.To improve the recovery,we concentrated SARS-CoV-2 viral particles and rna from both the solid and aqueous phases of wastewater using an electronegative membrane(EM).The captured viral particles and rna on the EM were incubated in our newly developed viral inactivation and rna preservation(VIP)buffer.Subsequently,the rna was concentrated on magnetic beads and inhibitors removed by washing.Without eluting,the rna on the magnetic beads was directly detected using reverse transcription quantitative polymerase chain reaction(RT-qPCR).Analysis of SARS-CoV-2 pseudovirus(SARS-CoV-2 rna in a noninfectious viral coat)spiked to wastewater samples showed an improved recovery of 80%.Analysis of 120 wastewater samples collected twice weekly between May 2021 and February 2022 from two wastewater treatment plants showed 100%positive detection,which agreed with the results independently obtained by a provincial public health laboratory.The concentrations of SARS-CoV-2 rna in these wastewater samples ranged from 2.4×10^(2) to 2.9×10^(6) copies per 100 mL of wastewater.Our method’s capability of detecting trace and diverse concentrations of SARS-CoV-2 in complex wastewater samples is attributed to the enhanced recovery of SARS-CoV-2 rna and efficient removal of PCR inhibitors.The improved method for the recovery and detection of viral rna in wastewater is important for wastewater surveillance,complementing clinical diagnostic tests for public health protection.

关键词： Wastewater Virus viral rna Environmental monitoring Pathogens Surveillance

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A COVID-19 Patient Discharged According to Strict Discharge Standards:viral Negativity in Both Nasopharynx and Feces

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Infectious Diseases & Immunity 2022年第3期2卷 210-212页

作者： Enqiang Chen Lichun Wang Guangming Tang Menglan Wang Yachao Tao Ping Feng Hong Tang Center of Infectious Diseases West China Hospital of Sichuan UniversityChengdu 610041China

Severe acute respiratory syndrome Coronavirus 2(SARS-CoV-2)currently has spread all over the world.However,the dynamic characteristics of SARS-CoV-2 infections have not previously been described in detail.Here,we report a cured patient in West China Hospital,and describe the dynamic detection of SARS-CoV-2-rna in different specimens and viral specific IgM and IgG antibodies in blood.The findings suggest that the fecal SARS-CoV-2-rna negativity may be considered as a new standard for de isolation.Serum IgM and IgG antibodies detection were helpful for early diagnosis of SARS-CoV-2 infection and judgment of patients in recovery stage,respectively.

关键词： Feces IgG antibody IgM antibody SARS-CoV-2 viral rna

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Retrospective Analysis of the Duration of Hospitalization of Imported Patients Infected with SARS-CoV-2 in Guangzhou, 2021

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Infectious Diseases & Immunity 2023年第1期3卷 36-39页

作者： Zhiwei Xie Guofang Tang Lu Li Jingrong Shi Qingxin Gan Xiaowen Zheng Jingyan Tang Huimin Zeng Chuyu Zhang Sisi Cheni Jianping Cui Zishi Lin Lihua Lin Youxia Li Jinxin Liu Feng Li Fengyu Hui Xiaoping Tang Xilong Deng Guangzhou Eighth People's Hospital Guangzhou Medical UniversityGuangzhou 510440China Guangzhou Laboratory Guangzhou 510440China.

The pandemic of coronavirus disease 2019 is“not over,”in fact,the“dynamic clearing”policy for SARS-CoV-2 control and prevention in China has been firmly enforced.This study aimed to analyze the clinical symptoms and dynamic viral rna changes in 2021 at Guangzhou Eighth People’s Hospital.This study showed that 31.4%of the patients(695/2212)tested negative for viral rna from admission to the final release from quarantine.Of all negative cases,86.5%(601/695)remained in the hospital for no more than 5 days and were asymptomatic or mild.Among the remaining 402 patients who stayed for no more than 5 days,76.4%(307/402)were viral rna retest positive during the isolation stage.However,96.4%of the peak viral rna(296/307)was over Ct=33 cycles during the isolation stage.

关键词： COVID-19 Imported Symptom viral rna

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RIG-I： a multifunctional protein beyond a pattern recognition receptor

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Protein & Cell 2018年第3期9卷 246-253页

作者： Xiao-xiao Xu Han Wan Li Nie Tong Shao Li-xin Xiang Jian-zhong Shao Key Laboratory for Cell and Gene Engineering of Zhejiang Province College of Life Sciences Zhejiang University Hangzhou 310058 China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Qingdao 266235 China

It was widely known that retinoic acid inducible gene I （RIG-I） functions as a cytosolic pattern recognition receptor that initiates innate antiviral immunity by detecting exogenous viral rnas. However, recent stud- ies showed that RIG-I participates in other various cellular activities by sensing endogenous rnas under different circumstances. For example, RIG-I facilitates the therapy resistance and expansion of breast cancer cells and promotes T cell-independent B cell activation through interferon signaling activation by recognizing non-coding rnas and endogenous retroviruses in certain situations. While in hepatocellular carcinoma and acute myeloid leukemia, RIG-I acts as a tumor suppressor through either augmenting STAT1 activation by competitively binding STAT1 against its negative regulator SliP1 or inhibiting AKT-mTOR signaling pathway by directly interacting with Src respectively. These new findings suggest that RIG-I plays more diverse roles in various cellular life activities, such as cell proliferation and differentiation, than previously known. Taken together, the function of RIG-I exceeds far beyond that of a pattern recognition receptor.

关键词： RIG-I viral rna endogenous rna immunity cancer

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Distinctive Drug-resistant Mutation Profiles and Interpretations of HIV-1 Proviral DNA Revealed by Deep Sequencing in Reverse Transcriptase

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Biomedical and Environmental Sciences 2016年第4期29卷 239-247页

作者： YIN Qian Qian LI Zhen Peng ZHAO Hai PAN Dong WANG Yan XU Wei Si XING Hui FENG Yi JIANG Shi Bo SHAO Yi Ming MA Li Ying State Key Laboratory of Infectious Disease Prevention and Control National Center for AIDS/STD Control and Prevention (NCAIDS) Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases Chinese Center for Disease Control and Prevention State Key Laboratory of Infectious Disease Prevention and Control National Institute for Communicable Disease Control and Prevention Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases Chinese Center for Disease Control and Prevention Key Laboratory of Medical Molecular Virology (Ministries of Education and Health) Shanghai Medical College and Institute of Medical Microbiology Fudan University

Objective To investigate distinctive features in drug-resistant mutations （DRMs） and interpretations for reverse transcriptase inhibitors （RTIs） between proviral DNA and paired viral rna in HIV-l-infected patients. Methods Forty-three HIV-l-infected individuals receiving first-line antiretroviral therapy were recruited to participate in a multicenter AIDS Cohort Study in Anhui and Henan Provinces in China in 2004. Drug resistance genotyping was performed by bulk sequencing and deep sequencing on the plasma and whole blood of 77 samples, respectively. Drug-resistance interpretation was compared between viral rna and paired proviral DNA. Results Compared with bulk sequencing, deep sequencing could detect more DRMs and samples with DRMs in both viral rna and proviral DNA. The mutations M1841 and M2301 were more prevalent in proviral DNA than in viral rna （Fisher＇s exact test, P〈0.05）. Considering ＇majority resistant variants＇, 15 samples （19.48%） showed differences in drug resistance interpretation between viral rna and proviral DNA, and 5 of these samples with different DRMs between proviral DNA and paired viral rna showed a higher level of drug resistance to the first-line drugs. Considering ＇minority resistant variants＇, 22 samples （28.57%） were associated with a higher level of drug resistance to the tested RTIs for proviral DNA when compared with paired viral rna. Conclusion Compared with viral rna, the distinctive information of DRMs and drug resistance interpretations for proviral DNA could be obtained by deep sequencing, which could provide more detailed and precise information for drug resistance monitoring and the rational design of optimal antiretroviral therapy regimens.

关键词： HIV-1 drug-resistant mutation Drug-resistance interpretation Proviral DNA viral rna Deep sequencing

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