Volume 221 of Issue 6 | The Journal of experimental medicine
Authors: Wu TT, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner WE, Kim PS, Blish CA, Krasnow MA
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.
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Critical care medicine
Authors: Makam AN, Burnfield J, Prettyman E, Nguyen OK, Wu N, Espejo E, Blat C, Boscardin WJ, Ely EW, Jackson JC, Covinsky KE, Votto J, Recovery After Transfer to an LTACH for COVID-19 (RAFT COVID) Study
Annals of the New York Academy of Sciences
Authors: Durstenfeld MS, Weiman S, Holtzman M, Blish C, Pretorius R, Deeks SG
The Lancet. Infectious diseases
Authors: Peluso MJ, Swank ZN, Goldberg SA, Lu S, Dalhuisen T, Borberg E, Senussi Y, Luna MA, Chang Song C, Clark A, Zamora A, Lew M, Viswanathan B, Huang B, Anglin K, Hoh R, Hsue PY, Durstenfeld MS, Spinelli MA, Glidden DV, Henrich TJ, Kelly JD, Deeks SG, Walt DR, Martin JN
Journal of clinical immunology
Authors: McDonnell J, Cousins K, Younger MEM, Lane A, Abolhassani H, Abraham RS, Al-Tamemi S, Aldave-Becerra JC, Al-Faris EH, Alfaro-Murillo A, AlKhater SA, Alsaati N, Doss AMA, Anderson M, Angarola E, Ariue B, Arnold DE, Assa'ad AH, Aytekin C, Bank M, Bergerson JRE, Bleesing J, Boesing J, Bouso C, Brodszki N, Cabanillas D, Cady C, Callahan MA, Caorsi R, Carbone J, Carrabba M, Castagnoli R, Catanzaro JR, Chan S, Chandra S, Chapdelaine H, Chavoshzadeh Z, Chong HJ, Connors L, Consonni F, Correa-Jimenez O, Cunningham-Rundles C, D'Astous-Gauthier K, Delmonte OM, Demirdag YY, Deshpande DR, Diaz-Cabrera NM, Dimitriades VR, El-Owaidy R, ElGhazali G, Al-Hammadi S, Fabio G, Faure AS, Feng J, Fernandez JM, Fill L, Franco GR, Frenck RW, Fuleihan RL, Giardino G, Galant-Swafford J, Gambineri E, Garabedian EK, Geerlinks AV, Goudouris E, Grecco O, Pan-Hammarström Q, Khani HHK, Hammarström L, Hartog NL, Heimall J, Hernandez-Molina G, Horner CC, Hostoffer RW, Hristova N, Hsiao KC, Ivankovich-Escoto G, Jaber F, Jalil M, Jamee M, Jean T, Jeong S, Jhaveri D, Jordan MB, Joshi AY, Kalkat A, Kanarek HJ, Kellner ES, Khojah A, Khoury R, Kokron CM, Kumar A, Lecerf K, Lehman HK, Leiding JW, Lesmana H, Lim XR, Lopes JP, López AL, Tarquini L, Lundgren IS, Magnusson J, Marinho AKBB, Marseglia GL, Martone GM, Mechtler AG, Mendonca L, Milner JD, Mustillo PJ, Naderi AG, Naviglio S, Nell J, Niebur HB, Notarangelo L, Oleastro M, Ortega-López MC, Patel NR, Petrovic G, Pignata C, Porras O, Prince BT, Puck JM, Qamar N, Rabusin M, Raje N, Regairaz L, Risma KA, Ristagno EH, Routes J, Roxo-Junior P, Salemi N, Scalchunes C, Schuval SJ, Seneviratne SL, Shankar A, Sherkat R, Shin JJ, Siddiqi A, Signa S, Sobh A, Lima FMS, Stenehjem KK, Tam JS, Tang M, Barros MT, Verbsky J, Vergadi E, Voelker DH, Volpi S, Wall LA, Wang C, Williams KW, Wu EY, Wu SS, Zhou JJ, Cook A, Sullivan KE, Marsh R
International journal of molecular sciences
Authors: Pulliam L, Sun B, McCafferty E, Soper SA, Witek MA, Hu M, Ford JM, Song S, Kapogiannis D, Glesby MJ, Merenstein D, Tien PC, Freasier H, French A, McKay H, Diaz MM, Ofotokun I, Lake JE, Margolick JB, Kim EY, Levine SR, Fischl MA, Li W, Martinson J, Tang N
Journal of general internal medicine
Authors: Conigliaro J, Elnicki DM, López L
Volume 20 of Issue 3 | PLoS pathogens
Authors: Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Bakhash SAM, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, Stone J, McDermot E, Truong M, Shendure J, Oltean HN, Viboud C, Chu H, Müller NF, Bedford T
SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.
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Critical care (London, England)
Authors: Ceccato A, Forne C, Bos LD, Camprubí-Rimblas M, Areny-Balagueró A, Campaña-Duel E, Quero S, Diaz E, Roca O, De Gonzalo-Calvo D, Fernández-Barat L, Motos A, Ferrer R, Riera J, Lorente JA, Peñuelas O, Menendez R, Amaya-Villar R, Añón JM, Balan-Mariño A, Barberà C, Barberán J, Blandino-Ortiz A, Boado MV, Bustamante-Munguira E, Caballero J, Carbajales C, Carbonell N, Catalán-González M, Franco N, Galbán C, Gumucio-Sanguino VD, de la Torre MDC, Estella Á, Gallego E, García-Garmendia JL, Garnacho-Montero J, Gómez JM, Huerta A, Jorge-García RN, Loza-Vázquez A, Marin-Corral J, Martínez de la Gándara A, Martin-Delgado MC, Martínez-Varela I, Messa JL, Muñiz-Albaiceta G, Nieto MT, Novo MA, Peñasco Y, Pozo-Laderas JC, Pérez-García F, Ricart P, Roche-Campo F, Rodríguez A, Sagredo V, Sánchez-Miralles A, Sancho-Chinesta S, Socias L, Solé-Violan J, Suarez-Sipmann F, Tamayo-Lomas L, Trenado J, Úbeda A, Valdivia LJ, Vidal P, Bermejo J, Gonzalez J, Barbe F, Calfee CS, Artigas A, Torres A, CIBERESUCICOVID Project
JMIR cardio
Authors: Park LG, Chi S, Pitsenbarger S, Johnson JK, Shah AJ, Elnaggar A, von Oppenfeld J, Cho E, Harzand A, Whooley MA
