World Health Organization. Weekly Epidemiological Update on COVID-19: 27 October 2023.; 2023. Accessed November 21, 2023. www.who.int/publications/m/item/covid-19-epidemiological-update---27-october-2023
Xu X, Chen P, Wang J, et al. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Sci China Life Sci. 2020;63(3):457–60. doi.org/10.1007/s11427-020-1637-5.
Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science. 2020;367(6485):1444–8. doi.org/10.1126/science.abb2762.
Chan JFW, Kok KH, Zhu Z, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect. 2020;9(1):221–36. doi.org/10.1080/22221751.2020.1719902.
Zandi M, Shafaati M, Kalantar-Neyestanaki D, et al. The role of SARS-CoV-2 accessory proteins in immune evasion. Biomed Pharmacother Biomedecine Pharmacother. 2022;156:113889. doi.org/10.1016/j.biopha.2022.113889.
Zandi M. ORF9c and ORF10 as accessory proteins of SARS-CoV-2 in immune evasion. Nat Rev Immunol. 2022;22(5):331. doi.org/10.1038/s41577-022-00715-2.
Wu F, Zhao S, Yu B, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265–9. doi.org/10.1038/s41586-020-2008-3.
To KKW, Sridhar S, Chiu KHY, et al. Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic. Emerg Microbes Infect. 2021;10(1):507–35. doi.org/10.1080/22221751.2021.1898291.
Docherty AB, Harrison EM, Green CA, et al. Features of 20 133 UK patients in hospital with COVID-19 using the ISARIC WHO clinical characterisation protocol: prospective observational cohort study. BMJ. 2020;369:m1985. doi.org/10.1136/bmj.m1985.
Richardson S, Hirsch JS, Narasimhan M, et al. Presenting characteristics, comorbidities, and outcomes among 5700 patients hospitalized with COVID-19 in the New York City area. JAMA. 2020;323(20):2052–9. doi.org/10.1001/jama.2020.6775.
Chung TWH, Sridhar S, Zhang AJ, et al. Olfactory dysfunction in coronavirus disease 2019 patients: observational cohort study and systematic review. Open Forum Infect Dis. 2020;7(6):199. doi.org/10.1093/ofid/ofaa199.
Aguilar RB, Hardigan P, Mayi B, et al. Current understanding of COVID-19 clinical course and investigational treatments. Front Med. 2020;7:555301. doi.org/10.3389/fmed.2020.555301.
Halpin S, O’Connor R, Sivan M. Long COVID and chronic COVID syndromes. J Med Virol. 2021;93(3):1242–3. doi.org/10.1002/jmv.26587.
Yong SJ. Long COVID or post-COVID-19 syndrome: putative pathophysiology, risk factors, and treatments. Infect Dis Lond Engl. 2021;53(10):737–54. doi.org/10.1080/23744235.2021.1924397.
Ren X, Zhou J, Guo J, et al. Reinfection in patients with COVID-19: a systematic review. Glob Health Res Policy. 2022;7(1):12. doi.org/10.1186/s41256-022-00245-3.
Quaranta EG, Fusaro A, Giussani E, et al. SARS-CoV-2 intra-host evolution during prolonged infection in an immunocompromised patient. Int J Infect Dis IJID Off Publ Int Soc Infect Dis. 2022;122:444–8. doi.org/10.1016/j.ijid.2022.06.023.
Nasir JA, Kozak RA, Aftanas P, et al. A comparison of whole genome sequencing of SARS-CoV-2 using amplicon-based sequencing, random hexamers, and bait capture. Viruses. 2020;12(8):E895. doi.org/10.3390/v12080895.
Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. Published 2010.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinforma Oxf Engl. 2014;30(15):2114–20. doi.org/10.1093/bioinformatics/btu170.
Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol J Comput Mol Cell Biol. 2012;19(5):455–77. doi.org/10.1089/cmb.2012.0021.
Deatherage DE, Barrick JE. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol Clifton NJ. 2014;1151:165–88. doi.org/10.1007/978-1-4939-0554-6_12.
Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15(11):524. doi.org/10.1186/s13059-014-0524-x.
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinforma Oxf Engl. 2014;30(9):1312–3. doi.org/10.1093/bioinformatics/btu033.
Liang W, Guan W, Chen R, et al. Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China. Lancet Oncol. 2020;21(3):335–7. doi.org/10.1016/S1470-2045(20)30096-6.
Martino R, Rámila E, Rabella N, et al. Respiratory virus infections in adults with hematologic malignancies: a prospective study. Clin Infect Dis Off Publ Infect Dis Soc Am. 2003;36(1):1–8. doi.org/10.1086/344899.
Hakki M, Rattray RM, Press RD. The clinical impact of coronavirus infection in patients with hematologic malignancies and hematopoietic stem cell transplant recipients. J Clin Virol Off Publ Pan Am Soc Clin Virol. 2015;68:1–5. doi.org/10.1016/j.jcv.2015.04.012.
Yonal-Hindilerden I, Hindilerden F, Mastanzade M, et al. Case report: Severe COVID-19 pneumonia in a patient with relapsed/refractory Hodgkin’s lymphoma. Front Oncol. 2021;11:601709. doi.org/10.3389/fonc.2021.601709.
Fakharian A, Ebrahimibagha H, Mirenayat MS, Farahmandi F. COVID-19 reinfection in a patient with Hodgkin lymphoma: a case report. Tanaffos. 2021;20(1):71–4.
Brouqui P, Colson P, Melenotte C, et al. COVID-19 re-infection. Eur J Clin Invest. 2021;51(5):e13537. doi.org/10.1111/eci.13537.
Chaguza C, Hahn AM, Petrone ME, et al. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MedRxiv Prepr Serv Health Sci. 2022. doi.org/10.1101/2022.06.29.22276868.
Dioverti V, Salto-Alejandre S, Haidar G. Immunocompromised patients with protracted COVID-19: a review of “long persisters.” Curr Transpl Rep. 2022;9(4):209–18. doi.org/10.1007/s40472-022-00385-y.
Baang JH, Smith C, Mirabelli C, et al. Prolonged severe acute respiratory syndrome coronavirus 2 replication in an immunocompromised patient. J Infect Dis. 2021;223(1):23–7. doi.org/10.1093/infdis/jiaa666.
Sepulcri C, Dentone C, Mikulska M, et al. The longest persistence of viable SARS-CoV-2 with recurrence of viremia and relapsing symptomatic COVID-19 in an immunocompromised patient-a case study. Open Forum Infect Dis. 2021;8(11):ofab217. doi.org/10.1093/ofid/ofab217.
Chen S, Guan F, Candotti F, et al. The role of B cells in COVID-19 infection and vaccination. Front Immunol. 2022;13:988536. doi.org/10.3389/fimmu.2022.988536.
Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol. 2023;95(1):e28138. doi.org/10.1002/jmv.28138.
Dejnirattisai W, Huo J, Zhou D, et al. SARS-CoV-2 Omicron-B1.1.529 leads to widespread escape from neutralizing antibody responses. Cell. 2022;185(3):467-484.e15. doi.org/10.1016/j.cell.2021.12.046.
Zhang L, Li Q, Liang Z, et al. The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron. Emerg Microbes Infect. 2022;11(1):1–5. doi.org/10.1080/22221751.2021.2017757.
Chavda VP, Bezbaruah R, Deka K, Nongrang L, Kalita T. The delta and omicron variants of SARS-CoV-2: what we know so far. Vaccines. 2022;10(11):1926. doi.org/10.3390/vaccines10111926.
Pulliam JRC, van Schalkwyk C, Govender N, et al. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science. 2022. doi.org/10.1126/science.abn4947.
Bakouny Z, Labaki C, Grover P, et al. Interplay of immunosuppression and immunotherapy among patients with cancer and COVID-19. JAMA Oncol. 2023;9(1):128–34. doi.org/10.1001/jamaoncol.2022.5357.
Liu C, Zhao Y, Okwan-Duodu D, Basho R, Cui X. COVID-19 in cancer patients: risk, clinical features, and management. Cancer Biol Med. 2020;17(3):519–27. doi.org/10.20892/j.issn.2095-3941.2020.0289.
Zhang L, Zhu F, Xie L, et al. Clinical characteristics of COVID-19-infected cancer patients: a retrospective case study in three hospitals within Wuhan, China. Ann Oncol Off J Eur Soc Med Oncol. 2020;31(7):894–901. doi.org/10.1016/j.annonc.2020.03.296.
Dai M, Liu D, Liu M, et al. Patients with cancer appear more vulnerable to SARS-CoV-2: a multicenter study during the COVID-19 outbreak. Cancer Discov. 2020;10(6):783–91. doi.org/10.1158/2159-8290.CD-20-0422.
Strasfeld L. COVID-19 and HSCT (Hematopoietic stem cell transplant). Best Pract Res Clin Haematol. 2022;35(3): 101399. doi.org/10.1016/j.beha.2022.101399.
Randi BA, Higashino HR, da Silva VP, Xavier EM, Rocha V, Costa SF. COVID-19 in hematopoietic stem-cell transplant recipients: a systematic review and meta-analysis of clinical characteristics and outcomes. Rev Med Virol. 2023;33(6):e2483. doi.org/10.1002/rmv.2483.
Abolghasemi S, Zolfaghari F, Naeimipoor M, Azhdari Tehrani H, Hakamifard A. COVID-19 reinfection or reactivation in a renal transplant patient. Clin Case Rep. 2021;9(8):e04672. doi.org/10.1002/ccr3.4672.
Côté F, Bestman-Smith J, Gourdeau M, et al. Reinfection with SARS-CoV-2 in a patient undergoing chemotherapy for lymphoma: Case report. J Assoc Med Microbiol Infect Dis Can J Off Assoc Pour Microbiol Medicale Infect Can. 2022;7(3):283–91. doi.org/10.3138/jammi-2021-0036.
McKittrick JM, Burke TW, Petzold E, et al. SARS-CoV-2 reinfection across a spectrum of immunological states. Health Sci Rep. 2022;5(4):e554. doi.org/10.1002/hsr2.554.
Avanzato VA, Matson MJ, Seifert SN, et al. Case study: Prolonged infectious SARS-CoV-2 shedding from an asymptomatic immunocompromised individual with cancer. Cell. 2020;183(7):1 1-1912.e9. doi.org/10.1016/j.cell.2020.10.049.
Cele S, Karim F, Lustig G, et al. SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape. Cell Host Microbe. 2022;30(2):154-162.e5. doi.org/10.1016/j.chom.2022.01.005.
Gandhi S, Klein J, Robertson AJ, et al. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Nat Commun. 2022;13(1):1547. doi.org/10.1038/s41467-022-29104-y.
Kemp SA, Collier DA, Datir RP, et al. SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2021;592(7853):277–82. doi.org/10.1038/s41586-021-03291-y.
Maponga TG, Jeffries M, Tegally H, et al. Persistent SARS-CoV-2 infection with accumulation of mutations in a patient with poorly controlled HIV infection. Clin Infect Dis Off Publ Infect Dis Soc Am. 2022. doi.org/10.1093/cid/ciac548.
Weigang S, Fuchs J, Zimmer G, et al. Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient as a source of immune escape variants. Nat Commun. 2021;12(1):6405. doi.org/10.1038/s41467-021-26602-3.
Canadian COVID-19 Genomics Network. Canadian VirusSeq data portal. virusseq-dataportal.ca/explorer.
