Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer
Victoria A Avanzato, M Jeremiah Matson, Stephanie N Seifert, Rhys Pryce, Brandi N Williamson, Sarah L Anzick, Kent Barbian, Seth D Judson, Elizabeth R Fischer, Craig Martens, Thomas A Bowden, Emmie de Wit, Francis X Riedo, Vincent J Munster, Victoria A Avanzato, M Jeremiah Matson, Stephanie N Seifert, Rhys Pryce, Brandi N Williamson, Sarah L Anzick, Kent Barbian, Seth D Judson, Elizabeth R Fischer, Craig Martens, Thomas A Bowden, Emmie de Wit, Francis X Riedo, Vincent J Munster
Abstract
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding was observed from the upper respiratory tract of a female immunocompromised individual with chronic lymphocytic leukemia and acquired hypogammaglobulinemia. Shedding of infectious SARS-CoV-2 was observed up to 70 days, and of genomic and subgenomic RNA up to 105 days, after initial diagnosis. The infection was not cleared after the first treatment with convalescent plasma, suggesting a limited effect on SARS-CoV-2 in the upper respiratory tract of this individual. Several weeks after a second convalescent plasma transfusion, SARS-CoV-2 RNA was no longer detected. We observed marked within-host genomic evolution of SARS-CoV-2 with continuous turnover of dominant viral variants. However, replication kinetics in Vero E6 cells and primary human alveolar epithelial tissues were not affected. Our data indicate that certain immunocompromised individuals may shed infectious virus longer than previously recognized. Detection of subgenomic RNA is recommended in persistently SARS-CoV-2-positive individuals as a proxy for shedding of infectious virus.
Keywords: COVID-19; SARS-CoV-2; asymptometic; chronic lymphocytic leukemia; convalescent plasma; immunocompromised; infectious virus; long-term shedding; within host evolution.
Conflict of interest statement
Declaration of Interests The authors declare no competing interests.
Published by Elsevier Inc.
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References
- Amanat F., Stadlbauer D., Strohmeier S., Nguyen T.H.O., Chromikova V., McMahon M., Jiang K., Arunkumar G.A., Jurczyszak D., Polanco J. A serological assay to detect SARS-CoV-2 seroconversion in humans. Nat. Med. 2020;26:1033–1036.
- Andrés C., Garcia-Cehic D., Gregori J., Piñana M., Rodriguez-Frias F., Guerrero-Murillo M., Esperalba J., Rando A., Goterris L., Codina M.G. Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients. Emerg. Microbes Infect. 2020;9:1900–1911.
- Baumann T., Delgado J., Montserrat E. CLL and COVID-19 at the Hospital Clinic of Barcelona: an interim report. Leukemia. 2020;34:1954–1956.
- Bhatraju P.K., Ghassemieh B.J., Nichols M., Kim R., Jerome K.R., Nalla A.K., Greninger A.L., Pipavath S., Wurfel M.M., Evans L. Covid-19 in Critically Ill Patients in the Seattle Region - Case Series. N. Engl. J. Med. 2020;382:2012–2022.
- Brouwer P.J.M., Caniels T.G., van der Straten K., Snitselaar J.L., Aldon Y., Bangaru S., Torres J.L., Okba N.M.A., Claireaux M., Kerster G. Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Science. 2020;369:643–650.
- Bullard J., Dust K., Funk D., Strong J.E., Alexander D., Garnett L., Boodman C., Bello A., Hedley A., Schiffman Z. Predicting infectious SARS-CoV-2 from diagnostic samples. Clin. Infect. Dis. 2020:ciaa638.
- Burbelo P.D., Riedo F.X., Morishima C., Rawlings S., Smith D., Das S., Strich J.R., Chertow D.S., Davey R.T., Jr., Cohen J.I. Detection of Nucleocapsid Antibody to SARS-CoV-2 is More Sensitive than Antibody to Spike Protein in COVID-19 Patients. medRxiv. 2020 2020.04.20.20071423.
- Capobianchi M.R., Rueca M., Messina F., Giombini E., Carletti F., Colavita F., Castilletti C., Lalle E., Bordi L., Vairo F. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy. Clin. Microbiol. Infect. 2020;26:954–956.
- CDC . 2020. Duration of Isolation and Precautions for Adults with COVID-19.
- CDC . 2020. People with Certain Medical Conditions.
- Chi X., Yan R., Zhang J., Zhang G., Zhang Y., Hao M., Zhang Z., Fan P., Dong Y., Yang Y. A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2. Science. 2020;369:650–655.
- Corman V.M., Landt O., Kaiser M., Molenkamp R., Meijer A., Chu D.K., Bleicker T., Brünink S., Schneider J., Schmidt M.L. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25:2000045.
- Corpet F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 1988;16:10881–10890.
- Fill L., Hadney L., Graven K., Persaud R., Hostoffer R. The clinical observation of a patient with common variable immunodeficiency diagnosed as having coronavirus disease 2019. Ann. Allergy Asthma Immunol. 2020;125:112–114.
- Fu Y., Han P., Zhu R., Bai T., Yi J., Zhao X., Tao M., Quan R., Chen C., Zhang Y. Risk factors for viral RNA shedding in COVID-19 patients. Eur. Respir. J. 2020;56 2001190.
- Fürstenau M., Langerbeins P., De Silva N., Fink A.M., Robrecht S., von Tresckow J., Simon F., Hohloch K., Droogendijk J., van der Klift M. COVID-19 among fit patients with CLL treated with venetoclax-based combinations. Leukemia. 2020;34:2225–2229.
- Gordon A. 2018. FASTX-Toolkit.
- Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010;59:307–321.
- Hadfield J., Megill C., Bell S.M., Huddleston J., Potter B., Callender C., Sagulenko P., Bedford T., Neher R.A. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34:4121–4123.
- Harcourt J., Tamin A., Lu X., Kamili S., Sakthivel S.K., Murray J., Queen K., Tao Y., Paden C.R., Zhang J. Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with Coronavirus Disease, United States. Emerg. Infect. Dis. 2020;26:1266–1273.
- He W., Chen L., Chen L., Yuan G., Fang Y., Chen W., Wu D., Liang B., Lu X., Ma Y. COVID-19 in persons with haematological cancers. Leukemia. 2020;34:1637–1645.
- He X., Lau E.H.Y., Wu P., Deng X., Wang J., Hao X., Lau Y.C., Wong J.Y., Guan Y., Tan X. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat. Med. 2020;26:672–675.
- Hoang D.T., Chernomor O., von Haeseler A., Minh B.Q., Vinh L.S. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol. Biol. Evol. 2018;35:518–522.
- Hu Z., Song C., Xu C., Jin G., Chen Y., Xu X., Ma H., Chen W., Lin Y., Zheng Y. Clinical characteristics of 24 asymptomatic infections with COVID-19 screened among close contacts in Nanjing, China. Sci. China Life Sci. 2020;63:706–711.
- Ikegami S., Benirschke R., Flanagan T., Tanna N., Klein T., Elue R., Debosz P., Mallek J., Wright G., Guariglia P. Persistence of SARS-CoV-2 nasopharyngeal swab PCR positivity in COVID-19 convalescent plasma donors. Transfusion. 2020 doi: 10.1111/trf.16015. Published online August 24, 2020.
- Broad Institute 2018. Picard Toolkit.
- Jary A., Leducq V., Malet I., Marot S., Klement-Frutos E., Teyssou E., Soulié C., Abdi B., Wirden M., Pourcher V. Evolution of viral quasispecies during SARS-CoV-2 infection. Clin. Microbiol. Infect. 2020 S1198-743X(20)30440-7.
- Jin X.H., Zheng K.I., Pan K.H., Xie Y.P., Zheng M.H. COVID-19 in a patient with chronic lymphocytic leukaemia. Lancet Haematol. 2020;7:e351–e352.
- Judson S.D., Munster V.J. A framework for nosocomial transmission of emerging coronaviruses. Infect. Control Hosp. Epidemiol. 2020:1–2.
- Kalyaanamoorthy S., Minh B.Q., Wong T.K.F., von Haeseler A., Jermiin L.S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017;14:587–589.
- Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 2013;30:772–780.
- Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–3066.
- Kim S.H., Ko J.H., Park G.E., Cho S.Y., Ha Y.E., Kang J.M., Kim Y.J., Huh H.J., Ki C.S., Jeong B.H. Atypical presentations of MERS-CoV infection in immunocompromised hosts. J. Infect. Chemother. 2017;23:769–773.
- Kim D., Lee J.Y., Yang J.S., Kim J.W., Kim V.N., Chang H. The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020;181:914–921.e10.
- Kunisaki K.M., Janoff E.N. Influenza in immunosuppressed populations: a review of infection frequency, morbidity, mortality, and vaccine responses. Lancet Infect. Dis. 2009;9:493–504.
- Lan L., Xu D., Ye G., Xia C., Wang S., Li Y., Xu H. Positive RT-PCR Test Results in Patients Recovered From COVID-19. JAMA. 2020;323:1502–1503.
- Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012;9:357–359.
- Lau S.Y., Wang P., Mok B.W., Zhang A.J., Chu H., Lee A.C., Deng S., Chen P., Chan K.H., Song W. Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction. Emerg. Microbes Infect. 2020;9:837–842.
- Lee S., Kim T., Lee E., Lee C., Kim H., Rhee H., Park S.Y., Son H.J., Yu S., Park J.W. Clinical Course and Molecular Viral Shedding Among Asymptomatic and Symptomatic Patients With SARS-CoV-2 Infection in a Community Treatment Center in the Republic of Korea. JAMA Intern Med. 2020;180:1–6.
- Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079.
- Li J., Zhang L., Liu B., Song D. Case Report: Viral Shedding for 60 Days in a Woman with COVID-19. Am. J. Trop. Med. Hyg. 2020;102:1210–1213.
- Liu L., Wang P., Nair M.S., Yu J., Rapp M., Wang Q., Luo Y., Chan J.F., Sahi V., Figueroa A. Potent Neutralizing Monoclonal Antibodies Directed to Multiple Epitopes on the SARS-CoV-2 Spike. bioRxiv. 2020 doi: 10.1101/2020.06.17.153486.
- Liu W.D., Chang S.Y., Wang J.T., Tsai M.J., Hung C.C., Hsu C.L., Chang S.C. Prolonged virus shedding even after seroconversion in a patient with COVID-19. J. Infect. 2020;81:318–356.
- Liu Y., Chen X., Zou X., Luo H. A severe-type COVID-19 case with prolonged virus shedding. J. Formos. Med. Assoc. 2020;119:1555–1557.
- Liu Z., Zheng H., Lin H., Li M., Yuan R., Peng J., Xiong Q., Sun J., Li B., Wu J. Identification of common deletions in the spike protein of SARS-CoV-2. J. Virol. 2020;94 e00790-20.
- Long Q.X., Tang X.J., Shi Q.L., Li Q., Deng H.J., Yuan J., Hu J.L., Xu W., Zhang Y., Lv F.J. Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections. Nat. Med. 2020;26:1200–1204.
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10–12.
- McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–1303.
- McMichael T.M., Clark S., Pogosjans S., Kay M., Lewis J., Baer A., Kawakami V., Lukoff M.D., Ferro J., Brostrom-Smith C. COVID-19 in a Long-Term Care Facility - King County, Washington, February 27-March 9, 2020. MMWR Morb. Mortal. Wkly. Rep. 2020;69:339–342.
- McMichael T.M., Currie D.W., Clark S., Pogosjans S., Kay M., Schwartz N.G., Lewis J., Baer A., Kawakami V., Lukoff M.D., Public Health–Seattle and King County, EvergreenHealth, and CDC COVID-19 Investigation Team Epidemiology of Covid-19 in a Long-Term Care Facility in King County, Washington. N. Engl. J. Med. 2020;382:2005–2011.
- Mira E., Yarce O.A., Ortega C., Fernández S., Pascual N.M., Gómez C., Alvarez M.A., Molina I.J., Lama R., Santamaria M. Rapid recovery of a SARS-CoV-2-infected X-linked agammaglobulinemia patient after infusion of COVID-19 convalescent plasma. J. Allergy Clin. Immunol. Pract. 2020;8:2793–2795.
- Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015;32:268–274.
- Paneesha S., Pratt G., Parry H., Moss P. Covid-19 infection in therapy-naive patients with B-cell chronic lymphocytic leukemia. Leuk. Res. 2020;93:106366.
- Prescott J., Falzarano D., de Wit E., Hardcastle K., Feldmann F., Haddock E., Scott D., Feldmann H., Munster V.J. Pathogenicity and Viral Shedding of MERS-CoV in Immunocompromised Rhesus Macaques. Front. Immunol. 2018;9:205.
- Qian G.Q., Chen X.Q., Lv D.F., Ma A.H.Y., Wang L.P., Yang N.B., Chen X.M. Duration of SARS-CoV-2 viral shedding during COVID-19 infection. Infect. Dis. (Lond.) 2020;52:511–512.
- Rambaut A., Holmes E.C., O’Toole Á., Hill V., McCrone J.T., Ruis C., du Plessis L., Pybus O.G. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 2020;5:1403–1407.
- Robert X., Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 2014;42 W320-4.
- Robinson J.T., Thorvaldsdóttir H., Wenger A.M., Zehir A., Mesirov J.P. Variant Review with the Integrative Genomics Viewer. Cancer Res. 2017;77:e31–e34.
- Sagulenko P., Puller V., Neher R.A. TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evol. 2018;4:vex042.
- Salazar E., Perez K.K., Ashraf M., Chen J., Castillo B., Christensen P.A., Eubank T., Bernard D.W., Eagar T.N., Long S.W. Treatment of Coronavirus Disease 2019 (COVID-19) Patients with Convalescent Plasma. Am. J. Pathol. 2020;190:1680–1690.
- Schubert M., Lindgreen S., Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes. 2016;9:88.
- Shen Z., Xiao Y., Kang L., Ma W., Shi L., Zhang L., Zhou Z., Yang J., Zhong J., Yang D. Genomic Diversity of Severe Acute Respiratory Syndrome-Coronavirus 2 in Patients With Coronavirus Disease 2019. Clin. Infect. Dis. 2020;71:713–720.
- Shu Y., McCauley J. GISAID: Global initiative on sharing all influenza data - from vision to reality. Euro Surveill. 2017;22:30494.
- Soresina A., Moratto D., Chiarini M., Paolillo C., Baresi G., Focà E., Bezzi M., Baronio B., Giacomelli M., Badolato R. Two X-linked agammaglobulinemia patients develop pneumonia as COVID-19 manifestation but recover. Pediatr. Allergy Immunol. 2020;31:565–569.
- Speranza E., Williamson B.N., Feldmann F., Sturdevant G.L., Pérez-Pérez L., Mead-White K., Smith B.J., Lovaglio J., Martens C., Munster V.J. SARS-CoV-2 infection dynamics in lungs of African green monkeys. bioRxiv. 2020 doi: 10.1101/2020.08.20.258087.
- Sun J., Xiao J., Sun R., Tang X., Liang C., Lin H., Zeng L., Hu J., Yuan R., Zhou P. Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids. Emerg. Infect. Dis. 2020;26:1834–1838.
- van der Vries E., Stittelaar K.J., van Amerongen G., Veldhuis Kroeze E.J., de Waal L., Fraaij P.L., Meesters R.J., Luider T.M., van der Nagel B., Koch B. Prolonged influenza virus shedding and emergence of antiviral resistance in immunocompromised patients and ferrets. PLoS Pathog. 2013;9:e1003343.
- van Kampen J.J.A., van de Vijver D.A.M.C., Fraaij P.L.A., Haagmans B.L., Lamers M.M., Okba N., van den Akker J.P.C., Endeman H., Gommers D.A.M.P.J., Cornelissen J.J. Shedding of infectious virus in hospitalized patients with coronavirus disease-2019 (COVID-19): duration and key determinants. medRxiv. 2020 doi: 10.1101/2020.06.08.20125310.
- Walls A.C., Park Y.J., Tortorici M.A., Wall A., McGuire A.T., Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell. 2020;181:281–292.e6.
- Wang Y., Grunewald M., Perlman S. Coronaviruses: An Updated Overview of Their Replication and Pathogenesis. Methods Mol. Biol. 2020;2203:1–29.
- Wang W., Xu Y., Gao R., Lu R., Han K., Wu G., Tan W. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. JAMA. 2020;323:1843–1844.
- Wölfel R., Corman V.M., Guggemos W., Seilmaier M., Zange S., Müller M.A., Niemeyer D., Jones T.C., Vollmar P., Rothe C. Virological assessment of hospitalized patients with COVID-2019. Nature. 2020;581:465–469.
- Wrapp D., Wang N., Corbett K.S., Goldsmith J.A., Hsieh C.L., Abiona O., Graham B.S., McLellan J.S. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science. 2020;367:1260–1263.
- Wrobel A.G., Benton D.J., Xu P., Roustan C., Martin S.R., Rosenthal P.B., Skehel J.J., Gamblin S.J. SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects. Nat. Struct. Mol. Biol. 2020;27:763–767.
- Zhu L., Xu X., Ma K., Yang J., Guan H., Chen S., Chen Z., Chen G. Successful recovery of COVID-19 pneumonia in a renal transplant recipient with long-term immunosuppression. Am. J. Transplant. 2020;20:1859–1863.
- Zou L., Ruan F., Huang M., Liang L., Huang H., Hong Z., Yu J., Kang M., Song Y., Xia J. SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N. Engl. J. Med. 2020;382:1177–1179.
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