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Recent Publications from PREPARE Institute Faculty

Here are a few of the hundreds of papers written or co-authored by our faculty. Click the links to view PubMed abstracts.


Bojórquez-Chapela I, Strathdee SA, Garfein RS, Benson CA, Chaillon A, Ignacio C, Sepulveda J. The impact of the COVID-19 pandemic among migrants in shelters in Tijuana, Baja California, Mexico. BMJ Glob Health. 2022;7(3):e007202. doi:10.1136/bmjgh-2021-007202. PMID35277428; PMC8919131.


Branche E, Wang YT, Viramontes K, Valls Cuevas JM, Xie J, Ana-Sosa-Batiz F, Shafee N, Duttke SH, McMillan RE, Clark E, Nguyen MN, Garretson AF, Crames JJ, J. SN, Zhu Z, Rich JN, Spector DH, Benner CB, Shresta S, Carlin AF. SREBP2-dependent lipid gene transcription enhances the infection of human dendritic cells by Zika virus. Nat Commun. 2022;13(1):5341. doi:doi: 10.1038/s41467-022-33041-1; PMID36097162.


Carter C, Akrami K, Hall D, Smith D, Aronoff-Spencer E. Lyophilized visually readable loop-mediated isothermal reverse transcriptase nucleic acid amplification test for detection Ebola Zaire RNA. J Virol Methods. 2017;244:32-38. doi:10.1016/j.jviromet.2017.02.013; PMID28242293; PMC5568651.


Chaillon A, Smith DM. Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution. Clin Infect Dis. 2021:73(12):2314-2317. doi:10.1093/cid/ciab265; PMID33772259; PMC8083653.


Chaillon A, Thurairajah PH, Hsiang JC, Martin NK. What is required for achieving hepatitis C virus elimination in Singapore? A modeling study. J Gastroenterol Hepatol. 2021;36(4):1110-1117. doi:10.1111/jgh.15211; PMID32777859; PMC8174139.


Chang, M.R., Tomasovic, L., Kuzmina, N.A. et al. IgG-like bispecific antibodies with potent and synergistic neutralization against circulating SARS-CoV-2 variants of concern. Nat Commun 13, 5814 (2022). PMID36192374; PMC9528872.


Karthikeyan S, Nguyen A, McDonald D, Zong Y, Ronquillo N, Ren J, Zou J, Farmer S, Humphrey G, Henderson D, Javidi T, Messer K, Anderson C, Schooley R, Martin NK, Knight R. Rapid, large-scale wastewater surveillance and automated reporting system enable early detection of nearly 85% of COVID-19 cases on a university campus. mSystems. 2021:00793-21:e0079321. doi:10.1128/mSystems.00793-21; PMID34374562.


Li N, Rana TM. Regulation of antiviral innate immunity by chemical modification of viral RNA. Wiley Interdiscip Rev RNA. 2022 Nov;13(6):e1720. doi: 10.1002/wrna.1720. Epub 2022 Feb 12. PMID: 35150188.


Li R, Mor M, Ma B, Clark AE, Alter J, Werbner M, Lee JC,  Leibel SL, Carlin AF, Dessau M, Gal-Tanamy M, Croker BA, Xiang Y, Freund NT. Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies. Commun Biol. 2022;5:789. doi:10.1038/s42003-022-03739-5. PMID35931732; PMC9355996.


Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Salas Garcia MC, Chiang LY, Salido RA, Shaffer JP, Bryant MK, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vazquez-Baeza Y, Torriani FJ, Knight R, Gilbert J, Sweeney DA, Allard SM. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment. Microbiome. 2021;9(1):132. doi:10.1186/s40168-021-01083-0; PMID34103074; PMC8186369.


Rawlings SA, Scott B, Layman L, Naranatt P, Heltsley R, Ignacio C, Porrachia M, Gianella S, Smith D, Chaillon A. Can't work from home: pooled nucleic acid testing of laboratory workers during the COVID-19 pandemic. Open Forum Infect Dis. 2021;8(7):ofab129. doi:10.1093/ofid/ofab129; PMID34327248; PMC7989168.


Schooley RT, Carlin AF, Beadle JR, Valiaeva N, Zhang XQ, Clark AE, McMillan RE, Leibel SL, McVicar RN, Xie J, Garretson AF, Smith VI, Murphy J, Hostetler KY. Rethinking Remdesivir: synthesis, antiviral activity and pharmacokinetics of oral lipid prodrugs. Antimicrob Agents Chemother. 2021:65(10):e0115521. doi:10.1128/AAC.01155-21; PMID34310217; PMC8448413.


Sette A, Crotty S. Immunological memory to SARS-CoV-2 infection and COVID-19 vaccines. Immunol Rev. 2022;310(1):27-46. doi: 10.1111/imr.13089; PMID35733376; PMC9349657


Singh NK, Ray P, Carlin AF, Magallanes C, Morgan SC, Laurent LC, Aronoff-Spencer ES, Hall DA. Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer. Biosens Bioelectron. 2021;180:113111. doi:10.1016/j.bios.2021.113111; PMID33743492; PMC7908832.


Strathdee SA, Abramovitz D, Harvey-Vera A, Vera CF, Rangel G, Artamonova I, Patterson TL, Mitchell RA, Bazzi AR. Correlates of Coronavirus Disease 2019 (COVID-19) Vaccine Hesitancy Among People Who Inject Drugs in the San Diego-Tijuana Border Region. Clin Infect Dis. 2022 Aug 24;75(1):e726-e733. doi: 10.1093/cid/ciab975. PMID35024825; PMC8690110.


Tarke A, Sidney J, Methot N, Yu ED, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, Wang E, Frazier A, Ramirez SI, Rawlings SA, Smith DM, da Silva Antunes R, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A. Impact of SARS-CoV-2 variants on the total CD4(+) and CD8(+) T cell reactivity in infected or vaccinated individuals. Cell Rep Med. 2021;2(7):100355. doi:10.1016/j.xcrm.2021.100355;  PMID34230917; PMC8249675.


Wang L, Sievert D, Clark AE, Lee S, Federman H, Gastfriend BD, Shusta EV, Palecek SP, Carlin AF, Gleeson JG. A human three-dimensional neural-perivascular 'assembloid' promotes astrocytic development and enables modeling of SARS-CoV-2 neuropathology. Nat Med. 2021: Online ahead of print. doi:10.1038/s41591-021-01443-1; PMID34244682.


Weintraub R, Plotkin S, Liu M, Kim J, Garcon N, Bell D, Storisteanu D, Norman T, Aronoff-Spencer E. COVID-19 vaccine delivery: an opportunity to set up systems for the future. Gates Open Res. 2020;4:182. doi:10.12688/gatesopenres.13210.2; PMID34124587; PMC8173566.