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COVER IMAGE Cover photograph: The basic pathophysiology of Mycobacterium tuberculosis infection is as follows. M. tuberculosis-containing aerosols are inhaled and reach the lungs. Following infection, macrophage recognition and bacterial engulfment trigger innate immune signaling pathways, which leads to recruitment of other immune cells (more macrophages, monocytes, neutrophils, natural killer cells, dendritic cells, and lymphocytes, etc.) to the infection site. These immune cells organize in a spherical structure, known as a granuloma, which typically suppresses the infection in its latent state (asymptomatic disease). can survive inside the granuloma for decades; however, environmental and/or genetic factors can cause the granuloma to disintegrate, allowing the bacilli to spread and form more lesions. This results in active tuberculosis (symptomatic disease), which can be transmitted to others. (See related article at e00036-20.) (Copyright © 2020 American Society for Microbiology. All Rights Reserved.)

EDITORIAL Corrella S. R The ASM Journals Committee Values the Contributions of Black Microbiologists e00203-20 Detweiler Editorial Patrick D. Schloss, Melissa Junior, Rebecca Alvania, Cesar A. Arias, Andreas Baumler, Arturo Casadevall, Corrella Detweiler, Harold Drake, Jack Gilbert, Michael J. Imperiale, Susan Lovett, Stanley Maloy, Alexander J. McAdam, Irene L. G. Newton, Michael J. Sadowsky, Rozanne M. Sandri-Goldin, Thomas J. Silhavy, Peter Tontonoz, Jo-Anne H. Young, Craig E. Cameron, Isaac Cann, A. Oveta Fuller, Ariangela J. Kozik

REVIEWS Jo-Anne H. Young R Beyond and Epstein-Barr : a Review of Composing e00027-20 REVIEW the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients Marie-Céline Zanella, Samuel Cordey, Laurent Kaiser Summary: Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the , Anelloviridae, , and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians’ radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.

Instructions to Authors are available on the journal website. CONTENTS • OCTOBER 2020 • VOLUME 33, NO. 4

Jo-Anne H. Young R Coronavirus Disease 2019–COVID-19 e00028-20 REVIEW Kuldeep Dhama, Sharun Khan, Ruchi Tiwari, Shubhankar Sircar, Sudipta Bhat, Yashpal Singh Malik, Karam Pal Singh, Wanpen Chaicumpa, D. Katterine Bonilla-Aldana, Alfonso J. Rodriguez-Morales Summary: In recent decades, several new diseases have emerged in different geographical areas, with pathogens including Ebola virus, Zika virus, Nipah virus, and coronaviruses (CoVs). Recently, a new type of viral infection emerged in Wuhan City, China, and initial genomic sequencing data of this virus do not match with previously sequenced CoVs, suggesting a novel CoV strain (2019-nCoV), which has now been termed severe acute respiratory syndrome CoV-2 (SARS-CoV-2). Although coronavirus disease 2019 (COVID-19) is suspected to originate from an host (zoonotic origin) followed by human-to-human transmission, the possibility of other routes should not be ruled out. Compared to diseases caused by previously known human CoVs, COVID-19 shows less severe pathogenesis but higher transmission competence, as is evident from the continuously increasing number of confirmed cases globally. Compared to other emerging viruses, such as Ebola virus, avian H7N9, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV), SARS- CoV-2 has shown relatively low pathogenicity and moderate transmissibility. Codon usage studies suggest that this novel virus has been transferred from an animal source, such as bats. Early diagnosis by real-time PCR and next-generation sequencing has facilitated the identification of the pathogen at an early stage. Since no antiviral drug or vaccine exists to treat or prevent SARS-CoV-2, potential therapeutic strategies that are currently being evaluated predominantly stem from previous experience with treating SARS-CoV, MERS- CoV, and other emerging viral diseases. In this review, we address epidemiological, diagnostic, clinical, and therapeutic aspects, including perspectives of vaccines and preventive measures that have already been globally recommended to counter this pandemic virus. Jo-Anne H. Young R The Echo of Pulmonary Tuberculosis: Mechanisms of Clinical Symptoms and e00036-20 REVIEW Other Disease-Induced Systemic Complications Laneke Luies, Ilse du Preez Summary: Clinical symptoms of active tuberculosis (TB) can range from a simple cough to more severe reactions, such as irreversible lung damage and, eventually, death, depending on disease progression. In addition to its clinical presentation, TB has been associated with several other disease-induced systemic complications, such as hyponatremia and glucose intolerance. Here, we provide an overview of the known, although ill-described, underlying biochemical mechanisms responsible for the clinical and systemic presentations associated with this disease and discuss novel hypotheses recently generated by various omics technologies. This summative update can assist clinicians to improve the tentative diagnosis of TB based on a patient’s clinical presentation and aid in the development of improved treatment protocols specifically aimed at restoring the disease-induced imbalance for overall homeostasis while simultaneously eradicating the pathogen. Furthermore, future applications of this knowledge could be applied to personalized diagnostic and therapeutic options, bettering the treatment outcome and quality of of TB patients. Jo-Anne H. Young R Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine e00053-19 REVIEW Identification of Bacteria in the Clinical Microbiology Laboratory Deirdre L. Church, Lorenzo Cerutti, Antoine Gürtler, Thomas Griener, Adrian Zelazny, Stefan Emler

Summary: This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and

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current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole- analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside. Jo-Anne H. Young R Convalescent Plasma Therapy for COVID-19: State of the Art e00072-20 REVIEW Daniele Focosi, Arthur O. Anderson, Julian W. Tang, Marco Tuccori Summary: Convalescent plasma (CP) therapy has been used since the early 1900s to treat emerging infectious diseases; its efficacy was later associated with the evidence that polyclonal neutralizing antibodies can reduce the duration of viremia. Recent large outbreaks of viral diseases for which effective antivirals or vaccines are still lacking has renewed the interest in CP as a life-saving treatment. The ongoing COVID-19 pandemic has led to the scaling up of CP therapy to unprecedented levels. Compared with historical usage, pathogen reduction technologies have now added an extra layer of safety to the use of CP, and new manufacturing approaches are being explored. This review summarizes historical settings of application, with a focus on betacoronaviruses, and surveys current approaches for donor selection and CP collection, pooling technologies, pathogen inactivation systems, and banking of CP. We additionally list the ongoing registered clinical trials for CP throughout the world and discuss the trial results published thus far.

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