Infectious disease
Abstract
BACKGROUND Accurate prognostic assays for COVID-19 represent an unmet clinical need. We sought to identify and validate early parsimonious transcriptomic signatures that accurately predict fatal outcomes.METHODS We studied 894 patients enrolled in the prospective, multicenter Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) with peripheral blood mononuclear cells (PBMC) and nasal swabs collected within 48 hours of admission. Host gene expression was measured with RNA-Seq. We trained parsimonious prognostic classifiers incorporating host gene expression, age, and SARS-CoV-2 viral load to predict 28-day mortality in 70% of the cohort. Classifier performance was determined in the remaining 30% and externally validated in a contemporary COVID-19 cohort (n = 137) with vaccinated patients.RESULTS Fatal COVID-19 was characterized by 4,189 differentially expressed genes in the peripheral blood. A COVID-specific 3-gene peripheral blood classifier (CD83, ATP1B2, DAAM2) combined with age and SARS-CoV-2 viral load achieved an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI, 0.82–0.94). A 3-gene nasal classifier (SLC5A5, CD200R1, FCER1A), in comparison, yielded an AUC of 0.74 (95% CI, 0.64–0.83). Notably, OLAH, the most strongly upregulated gene in both PBMC and nasal swab and recently implicated in severe viral infection pathogenesis, yielded AUCs of 0.86 (0.79–0.93) and 0.78 (95% CI, 0.69–0.86), respectively. Both peripheral blood classifiers demonstrated comparable performance in an independent contemporary cohort of vaccinated patients (AUCs 0.74–0.80).CONCLUSION Our parsimonious blood- and nasal-based classifiers accurately predicted COVID-19 mortality and merit further study as accessible prognostic tools to guide triage, resource allocation, and early therapeutic interventions.FUNDING NIH: 5R01AI135803-03, R35HL140026, 5U19AI118608-04, 5U19AI128910-04, 4U19AI090023-11, 4U19AI118610-06, R01AI145835-01A1S1, 5U19AI062629-17, 5U19AI057229-17, 5U19AI125357-05, 5U19AI128913-03, 3U19AI077439-13, 5U54AI142766-03, 5R01AI104870-07, 3U19AI089992-09, 3U19AI128913-03, 5T32DA018926-18, and K0826161611. National Institute of Allergy and Infectious Diseases, NIH: 3U19AI1289130, U19AI128913-04S1, and R01AI122220. National Center for Advancing Translational Sciences, NIH: UM1TR004528. The National Science Foundation: DMS2310836. The Chan Zuckerberg Biohub San Francisco.
Authors
Rithwik Narendra, Emily C. Lydon, Hoang Van Phan, Natasha Spottiswoode, Lucile P. Neyton, Joann Diray-Arce, IMPACC Network, COMET Consortium, EARLI Consortium, Patrice M. Becker, Seunghee Kim-Schulze, Annmarie Hoch, Harry Pickering, Patrick van Zalm, Charles B. Cairns, Matthew C. Altman, Alison D. Augustine, Steve Bosinger, Walter Eckalbar, Leying Guan, Naresh Doni Jayavelu, Steven H. Kleinstein, Florian Krammer, Holden T. Maecker, Al Ozonoff, Bjoern Peters, Nadine Rouphael, Ruth R. Montgomery, Elaine Reed, Joanna Schaenman, Hanno Steen, Ofer Levy, Sidney C. Haller, David Erle, Carolyn M. Hendrickson, Matthew F. Krummel, Michael A. Matthay, Prescott Woodruff, Elias K. Haddad, Carolyn S. Calfee, Charles R. Langelier
Abstract
Despite the widespread use of adenovirus, mRNA, and protein-based vaccines during the COVID-19 pandemic, their relative immunological profiles and protective efficacies remain incompletely defined. Here, we compared antigen kinetics, innate and adaptive immune responses, and protective efficacy following Ad5, mRNA, and protein vaccination in mice. Ad5 induced the most sustained antigen expression, but mRNA induced the most potent IFN responses, associated with robust antigen presentation and costimulation. Unlike Ad5 vaccines, which were hindered by preexisting vector immunity, mRNA vaccines retained efficacy after repeated use. As a single-dose regimen, Ad5 vaccines elicited higher immune responses. However, as a prime-boost regimen, and particularly in Ad5 seropositive mice, mRNA vaccines were more immunogenic than the other vaccine platforms. These findings highlight strengths of each vaccine platform and underscore the importance of host serostatus in determining optimal vaccine performance.
Authors
Bakare Awakoaiye, Shiyi Li, Sarah Sanchez, Tanushree Dangi, Nahid Irani, Laura Arroyo, Gabriel Arellano, Shadi Mohammadabadi, Malika Aid, Pablo Penaloza-MacMaster
Abstract
Elite controllers (ECs) maintain undetectable levels of plasma viremia in the absence of treatment, but small reservoirs of replication-competent proviruses persist in the vast majority of these persons. We longitudinally studied paired blood and inguinal lymph node samples (LNMC) from two ECs to better characterize distinguishing features of viral reservoir cell dynamics in ECs. In both participants, we observed a 7- to 10-fold lower frequency of intact proviruses in LNMC samples relative to reservoir cells circulating in blood. The landscape of intact proviruses in both tissue compartments was dominated by shared large clones that were frequently integrated in non-coding DNA regions, but the frequency and diversity of intact proviruses was more limited in LNMCs. Of note, over 9-10 years of longitudinal follow-up, a 3- to 18-fold reduction of intact proviruses was observed. Together, these data support the hypothesis that viral reservoirs in ECs’ blood and lymphoid tissues are under strong, likely immune-mediated selection pressure.
Authors
Samantha K. Marzi, Chloé M. Naasz, Leah Carrere, Carmen Gasca-Capote, Isabelle C. Roseto, Ce Gao, Matthias Cavassini, Andrea Mastrangelo, Mathias Lichterfeld, Matthieu Perreau, Xu G. Yu
Abstract
High-affinity antibody production depends on CD4+ T-follicular helper (Tfh) cells. In humans, peripheral blood Tfh cells are heterogenous, as evidenced by differential expression of the chemokine receptors, CXCR3 and CCR6, which to date have served to classify three subsets, pTfh1, pTfh2 and pTfh17. Although pTfh1 responses dominate during blood-stage Plasmodium infections, a clear association with protective antibody responses remains to be described. We hypothesise that pTfh cells exhibit greater phenotypic and functional heterogeneity than that described by CXCR3/CCR6 alone, and that these more nuanced pTfh subsets play distinct roles during Plasmodium infection. We map pTfh cell heterogeneity in healthy individuals prior to and during controlled human malaria infection (CHMI) using parallel scRNA-seq and VDJ-seq. We uncover two pTfh1 subsets or differential phenotypic states, distinguishable by CCR7 expression. Prior to infection, Tfh1-CCR7neg cells exhibit higher baseline expression of inflammatory cytokines and genes associated with cytotoxicity. While Tfh1-CCR7pos cells have higher GC signatures. Indeed, during CHMI, Tfh1-CCR7pos, Tfh1-CCR7neg, and Tfh2 cells, all clonally expand and become activated. However, only Tfh1-CCR7pos and Tfh2 cells positively associate with protective antibody production. Hence, our data reveal further complexity amongst human Tfh cells, and highlight two distinct subsets associated with antibody-mediated immunity to malaria.
Authors
Megan S.F. Soon, Damian A. Oyong, Nicholas L. Dooley, Reena Mukhiya, Zuleima Pava, Dean Andrew, Jessica R. Loughland, James S. McCarthy, Jo-Anne Chan, James G. Beeson, Christian Engwerda, Ashraful Haque, Michelle J. Boyle
Abstract
Acute lower respiratory infections are the primary cause of global mortality in post-neonatal children. Most respiratory viruses primarily involve upper airway infection and inflammation, yet nasal responses are poorly characterized. Using a mouse model of human metapneumovirus (HMPV), we found viral burden was higher in nasal airways and exhibited delayed clearance. Despite high burden, there was low nasal expression of type I and III interferon (IFN). Single-cell RNA-sequencing (scRNA-seq) from HMPV-infected mice showed lower nasal interferon-stimulated gene (ISG) expression and nasal enrichment of genes negatively regulating IFN. scRNA-seq of COVID-19 patients confirmed lower ISG expression in upper airways. HMPV infection downregulated nasal expression of interferon regulatory factor-3, suggesting a mechanism for limited response. To rescue the quiescent environment, we administered type I or III IFN to upper airways early post-infection, leading to lower nasal HMPV titer and virus-specific CD8+ T-cell upregulation. Intranasal immunization adjuvanted with type I or III IFN improved immune response, reduced clinical disease, and enhanced viral clearance in HMPV and influenza infection. IFN adjuvant increased recruitment of dendritic cells, resident-memory T-cells, and neutralizing antibodies. These findings reveal locally suppressed IFN production contributes to a quiescent nasal immune landscape that delays viral clearance and impairs mucosal vaccine responses.
Authors
Jorna Sojati, Olivia B. Parks, Taylor Eddens, Jie Lan, Monika Johnson, John V. Williams
Abstract
Background. The SARS-CoV-2 virus has evolved subvariants since the emergence of the omicron variant in 2021. Whether these changes impact viral shedding and transmissibility is not known. Methods. POSITIVES is a prospective longitudinal cohort of individuals with mild SARS-CoV-2 infection. Ambulatory, immunocompetent participants who did not receive antivirals self-administered 6 anterior nasal swabs over 15 days. Samples were analyzed by qPCR to quantify viral RNA, semi-quantitative viral culture to detect shedding of replication-competent virus, and whole genome sequencing to classify subvariants. Our predictor of interest was omicron subvariant: BA.1x, BA.2x, BA.4/5x, XBB.x and JN.x. Outcomes included RNA levels and duration of shedding replication-competent virus. We additionally explored whether the duration and severity of symptom correlated with duration of viral shedding and whether symptoms are a valid marker for ending isolation. Results. The median peak nasal SARS-CoV-2 RNA (6.0-6.3 log10 RNA copies/mL), median days to peak RNA (4-5 days), median days to undetectable viral RNA (10-12 days) and median days to negative viral culture (3.5-6 days) was similar across omicron subvariants. Number and severity of symptoms were also similar. For all subvariants, a sizeable percentage (range 28.2-52.0%) shed replication-competent virus after fever resolution and improvement of symptoms. Conclusion. Despite ongoing viral evolution, key aspects of viral dynamics of SARS-CoV-2 infection, including the duration of shedding replication-competent virus, have not substantially changed across omicron subvariants. Replication-competent shedding of these subvariants is detected for a large proportion of people who meet criteria for ending isolation. Funding. This work was supported by the National Institutes of Health (NIH), the Massachusetts Consortium on Pathogen Readiness, and the Massachusetts General Hospital Department of Medicine.
Authors
Julie Boucau, Owen T. Glover, Caitlin Marino, Gregory E. Edelstein, Manish C. Choudhary, Yijia Li, Brooke M. Leeman, Zahra Reynolds, Karry Su, Dessie Tien, Chase B. Mandell, Eliza Passell, Andrew Alexandrescu, Emory Abar, Mamadou Barry, Dibya Ghimire, Tammy D. Vyas, Jatin M. Vyas, Jacob E. Lemieux, Jonathan Z. Li, Mark J. Siedner, Amy K. Barczak
Bcl6 reactivity is associated with a distinct immune landscape and spatial transcriptome in COVID-19
Abstract
The regulation of follicular (F) and germinal center (GC) immune reactivity in human lymph nodes (LNs), particularly during the acute stages of viral infection, remains poorly understood: We have analyzed lung-draining lymph nodes (LD-LNs) from COVID-19 autopsies using multiplex imaging and spatial transcriptomics to examine the immune landscape with respect to follicular immune reactivity. We identified three groups of donors based on the Bcl6 prevalence of their Reactive Follicles (RFs): RF-Bcl6no/low, RF-Bcl6int, and RF-Bcl6high. A distinct B/TFH immune landscape, associated with increased prevalence of proliferating B-cell and TFH-cell subsets, was found in RF-Bcl6high LD-LNs. The comparison between LD-LNs and subdiaphragmatic (SD) LNs from the same donor revealed a divergent Bcl6 expression between the two anatomical sites. LD-LN Bcl6 expression was also associated with a distinct spatial transcriptomic profile. TH1-associated genes/pathways (e.g., CXCR3, STAT5, TNF-signaling) were significantly up-regulated in RF-Bcl6no/low tissues, while the RF-Bcl6high tissues exhibited significant up-regulation of GC-promoting genes/pathways (e.g., CXCL13, B-cell receptor signaling). Our findings reveal a heterogeneous F/GC landscape in COVID-19 LD-LNs, highlighting specific molecular targets and pathways that could regulate human F/GC immune dynamics during acute viral infections.
Authors
Cloé Brenna, Bernat Bramon Mora, Kalliopi Ioannidou, Julien Bodelet, Mia L. Siebmanns, Simon Burgermeister, Spiros Georgakis, Michail Orfanakis, Yannick D. Muller, Nazanin Sédille, Matthew J. Feinstein, Jon W. Lomasney, Oliver Y. Chén, Giuseppe Pantaleo, Sabina Berezowska, Laurence de Leval, Raphael Gottardo, Constantinos Petrovas
Abstract
BACKGROUND. Understanding age-associated differences in acute and memory adaptive immunity to SARS-CoV-2 and how this contributes to more favorable outcomes in children is critically important. METHODS. We evaluated SARS-CoV-2–specific T cell, B cell, and antibody responses in 329 peripheral blood samples collected from non-hospitalized children, adolescents, and adults at three timepoints, including acute and memory timepoints. RESULTS. Most children produced robust CD4+ T cell responses during infection and developed memory CD4+ T cells; however, young children <4 years old often had undetectable CD4+ T cell responses compared to older children and adults. Young children also generated reduced frequencies of memory B cells; despite this, they mounted substantial and durable neutralizing antibody responses. CD4+ T cell responses in children were biased towards non-spike epitopes, especially in asymptomatic cases. Memory B cells in children were preferentially classical memory or, paradoxically, CXCR3+. CONCLUSION. These findings support the concept that the kinetics and composition of T and B cell responses shift across age groups and may be associated with milder COVID-19 outcomes in children.
Authors
L. Benjamin Hills, Numana Bhat, Jillian H. Hurst, Amber Myers, Thomas W. Burke, Micah T. McClain, Elizabeth Petzold, Alexandre T. Rotta, Nicholas A. Turner, Alba Grifoni, Daniela Weiskopf, Yvonne Dogariu, Genevieve G. Fouda, Sallie R. Permar, Alessandro Sette, Christopher W. Woods, Matthew S. Kelly, Shane Crotty
Abstract
To radically diminish TB incidence and mortality by 2035, as set out by the WHO End TB Strategy, there is a desperate need for improved TB therapies and a more effective vaccine against the deadly pathogen Mycobacterium tuberculosis (Mtb). Aerosol vaccination with the MtbΔsigH mutant protects two different species of NHPs against lethal TB challenge by invoking vastly superior T and B cell responses in the lungs through superior antigen-presentation and interferon-conditioning. Since the Geneva consensus on essential steps towards the development of live mycobacterial vaccines recommends that live TB vaccines must incorporate at least two independent gene knock outs, we have now generated several rationally designed, double (DKO)- and triple (TKO) knock-out mutants in Mtb, each containing the ΔsigH deletion. Here, we report preclinical studies in the rhesus macaque model of aerosol infection and SIV/HIV co-infection, aimed at assessing the safety of these MtbΔsigH - based DKOs and TKOs. We found that most of these mutant strains are attenuated in both immunocompetent and SIV-co-infected macaques and combinatorial infection with these generated strong cellular immune responses in the lung, akin to MtbΔsigH. Aerosol infection with these KO strains elicited inducible Bronchus Associated Lymphoid Tissue (iBALT), which is a correlate of protection from TB.
Authors
Garima Arora, Caden W. Munson, Mushtaq Ahmed, Vinay Shivanna, Annu Devi, Venkata S.R. Devireddy, Basil Antony, Shannan Hall-Ursone, Olga D. Gonzalez, Edward Dick Jr., Chinnaswamy Jagannath, Xavier Alvarez, Smriti Mehra, Shabaana A. Khader, Dhiraj K. Singh, Deepak Kaushal
Abstract
Exposure to Bacillus Calmette-Guérin (BCG) or Canarypox ALVAC/Alum vaccine elicits pro- or antiinflammatory innate responses, respectively. We tested whether prior exposure of macaques to these immunogens protected against SARS-CoV-2 replication in lungs and found more efficient replication control after the pro-inflammatory immunity elicited by BCG. The decreased virus level in lungs was linked to early infiltrates of classical monocytes producing IL-8 with systemic neutrophils, Th2 cells, and Ki67+CD95+CD4+ T cells producing CCR7. At the time of SARS-CoV-2 exposure, BCG-treated animals had higher frequencies of lung infiltrating neutrophils and higher CD14+ cells expressing efferocytosis marker MERTK, responses correlating with decreased SARS-CoV-2 replication in lung. At the same time point, plasma IL-18, TNF-α, TNFSF-10, and VEGFA levels were also higher in the BCG group and correlated with decreased virus replication. Finally, after SARS-CoV-2 exposure, decreased virus replication correlated with neutrophils producing IL-10 and CCR7 preferentially recruited to the lungs of BCG-vaccinated animals. These data point to the importance of the spatiotemporal distribution of functional monocytes and neutrophils in controlling SARS-CoV-2 levels and suggest a central role of monocyte efferocytosis in curbing replication.
Authors
Mohammad Arif Rahman, Katherine C. Goldfarbmuren, Sarkis Sarkis, Massimiliano Bissa, Anna Gutowska, Luca Schifanella, Ramona Moles, Melvin N. Doster, Hanne Andersen, Yogita Jethmalani, Leonid Serebryannyy, Timothy Cardozo, Mark G. Lewis, Genoveffa Franchini
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