Publication

Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater

Xingwen Chen, John Balliew, Cici X Bauer, Jennifer Deegan, Anna Gitter, Blake M Hanson, Anthony W Maresso, Michael J Tisza, Catherine L Troisi, Janelle Rios, Kristina D Mena, Eric Boerwinkle, Fuqing Wu*

Journal of Infection, 2024, https://doi.org/10.1016/j.jinf.2024.106284.

Sequencing-based detection of Avian influenza A (H5N1) virus in wastewater in ten Cities

Michael J Tisza, Blake M Hanson, Justin R Clark, Li Wang, Katelyn Payne, Matthew C Ross, Kristina D Mena, Anna Gitter, Sara J Javornik Cregeen, Juwan Cormier, Vasanthi Avadhanula, Austen Terwilliger, John Balliew, Fuqing Wu, Janelle Rios, Jennifer Deegan, Pedro A Piedra, Joseph F Petrosino, Eric Boerwinkle, Anthony W Maresso

New England Journal of Medicine, 2024, DOI: 10.1056/NEJMc2405937.

Primers and probes for the diagnostics of mpox virus.

Xingwen Chen, Jiaoyang Xu, Scout Vanderwal, Fuqing Wu*

The Scientific Basis of Mpox (Monkeypox), 2024, Elsevier, p. 227-240.

Eye infection risks from Pseudomonas aeruginosa via hand soap and eye drops

Anna Gitter  Kristina D. Mena, Karla S. Mendez, Fuqing Wu, Charles P. Gerba

Applied and Environmental Microbiology, 2024, https://doi.org/10.1128/aem.02119-23.

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Xiaoqian Annie Yu, Craig McLean, Jan-Hendrik Hehemann, David Angeles-Albores, Fuqing Wu, Artur Muszynski, Christopher H. Corzett, Parastoo Azadi, Elizabeth B. Kujawinski, Eric J. Alm, Martin F. Polz

The ISME Journal, 2024, https://doi.org/10.1093/ismejo/wrad013.

Wastewater analysis of mpox virus in a city with low prevalence of Mpox disease: an environmental surveillance study

Jeremiah Oghuan, Carlos Chavarria, Scout R. Vanderwal, Anna Gitter, Akpevwe Amanda Ojaruega, Carlos Monserrat, Cici X. Bauer, Eric L. Brown, Sara Javornik Cregeen, Jennifer Deegan, Blake M. Hanson, Michael Tisza, , Hector I Ocaranza, John Balliew, Anthony W. Maresso, Janelle Rios, Eric Boerwinkle, Kristina D. Mena*, Fuqing Wu*

The Lancet Regional Health - Americas, 2023, https://doi.org/10.1016/j.lana.2023.100639.

Wastewater sequencing reveals community and variant dynamics of the collective human virome

Michael Tisza, Sara Javornik Cregeen, Vasanthi Avadhanula, Ping Zhang, Tulin Ayvaz, Karen Feliz, Kristi L. Hoffman, Justin R. Clark, Austen Terwilliger, Matthew C. Ross, Juwan Cormier, Hannah Moreno, Li Wang, Katelyn Payne, David Henke, Catherine Troisi, Fuqing Wu, Janelle Rios, Jennifer Deegan, Blake Hansen, John Balliew, Anna Gitter, Kehe Zhang, Runze Li, Cici X. Bauer, Kristina D. Mena, Pedro A. Piedra, Joseph F. Petrosino, Eric Boerwinkle & Anthony W. Maresso

Nature Communication, 2023, https://doi.org/10.1038/s41467-023-42064-1.

Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks

Tin Phan, Samantha Brozak, Bruce Pell, Jeremiah Oghuan, Anna Gitter, Tao Hu, Ruy M. Ribeiro, Ruian Ke, Kristina D. Mena, Alan S. Perelson, Yang Kuang, Fuqing Wu*

Water Research, 2023, https://doi.org/10.1016/j.watres.2023.120372. [pdf]

Surveillance of SARS-CoV-2 in Wastewater at the Population Level: Insights into the Implementation of Non-invasive Targeted Monitoring in Singapore and the USA

M. Leifels, W. L. Lee, F. Armas, X. Gu, F. Chandra, D. Cheng, W. C. Kwok, D. Chua, S. Y. Kim, W. J. Ng, D. Nainai, K. Sirikanchana, E. Sozzi, A. H. Farnleitner, F. Wu, S. Wuertz, and J. Thompson

The Handbook of Environmental Chemistry (Springer, Berlin, Heidelberg), 2023, https://doi.org/10.1007/698_2023_988.

The emergence of a virus variant: dynamics of a competition model with cross-immunity time-delay validated by wastewater surveillance data for COVID-19

Bruce Pell, Samantha Brozak, Tin Phan, Fuqing Wu & Yang Kuang

Journal of Mathematical Biology, 2023, https://doi.org/10.1007/s00285-023-01900-0.

Updated analysis to reject the laboratory-engineering hypothesis of SARS-CoV-2

Fuqing Wu

Environmental Research, 2023, https://doi.org/10.1016/j.envres.2023.115481.

Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program

Justin R. Clark†, Austen Terwilliger†, Vasanthi Avadhanula†, Michael Tisza, Juwan Cormier, Sara Javornik-Cregeen, Matthew Clayton Ross, Kristi Louise Hoffman, Catherine Troisi, Blake Hanson, Joseph Petrosino, John Balliew, Pedro A. Piedra, Janelle Rios, Jennifer Deegan, Cici Bauer, Fuqing Wu, Kristina D. Mena, Eric Boerwinkle and Anthony W. Maresso on behalf of TEPHI Wastewater Consortium

Frontiers in Public Health, 2023, https://doi.org/10.3389/fpubh.2023.1137881.

Not a waste: wastewater surveillance to enhance public health

Anna Gitter†, Jeremiah Oghuan†, Anuja Rajendra Godbole†, Carlos A. Chavarria, Carlos Monserrat, Tao Hu, Yun Wang, Anthony W. Maresso, Blake M. Hanson, Kristina D. Mena, Fuqing Wu*

Frontiers in Chemical Engineering (Environmental Chemical Engineering section), 2023, https://doi.org/10.3389/fceng.2022.1112876.

Assessment of a SARS-CoV-2 wastewater monitoring program in El Paso, Texas, from November 2020 to June 2022

Anna Gitter, Cici Bauer, Fuqing Wu, Ryan Ramphul, Carlos Chavarria, Kehe Zhang, Joseph Petrosino, Melissa Mezzari, Gabriela Gallegos, Austen L. Terwilliger, Justin R. Clark, Karen Feliz, Vasanthi Avadhanula, Tony Piedra, Kyle Weesner, Anthony Maresso, Kristina D. Mena

International Journal of Environmental Health Research. 2023, https://doi.org/10.1080/09603123.2022.2159017 

Wide mismatches in the sequence of primers and probes for monkeypox virus diagnostic assays

Fuqing Wu*, Jeremiah Oghuan, Anna Gitter, Kristina D. Mena, Eric L. Brown

Journal of Medical Virology, 2022, https://doi.org/10.1002/jmv.28395.

A simple SEIR-V model to estimate COVID-19 prevalence and predict SARS-CoV-2 transmission using wastewater-based surveillance data

Tin Phan, Samantha Brozak, Bruce Pell, Anna Gitter, Amy Xiao, Kristina D. Mena, Yang Kuang*, Fuqing Wu*

Science of The Total Environment, 2022, https://doi.org/10.1016/j.scitotenv.2022.159326.

Maternal Microbiota Modulate a Fragile X-like Syndrome in Offspring Mice

Bernard J. Varian, Katherine T. Weber, Lily J. Kim, Tony E. Chavarria, Sebastian E. Carrasco, Sureshkumar Muthupalani, Theofilos Poutahidis, Marwa Zafarullah, Reem R. Al Olaby, Mariana Barboza, Kemal Solakyildirim, Carlito Lebrilla, Flora Tassone, Fuqing Wu, Eric J. Alm, Susan E. Erdman

Genes, 2022, 13(8), 1409; https://doi.org/10.3390/genes13081409

Monitoring human arboviral diseases through wastewater surveillance: Challenges, progress and future opportunities

Wei Lin Lee, Xiaoqiong Gu, Federica Armas, Mats Leifels, Fuqing Wu, Franciscus Chandra, Feng Jun, Desmond Chua, Ayesa Syenina, Hongjie Chen, Dan Cheng, Eng Eong Ooi, Stefan Wuertz, Eric J Alm, Janelle Thompson

Water Research, 2022, https://doi.org/10.1016/j.watres.2022.118904

Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Wei Lin Lee, Federica Armas, Flavia Guarneri, Xiaoqiong Gu, Nicoletta Formenti, Fuqing Wu, Franciscus Chandra, Giovanni Parisio, Hongjie Chen, Amy Xiao,  Claudia Romeo, Federico Scali, Matteo Tonni, Mats Leifels, Feng Jun, Desmond Chua, Germaine WC Kwok, Joey YR Tay, Paolo, Pasquali, Janelle Thompson, Giovanni Loris, Alborali, Eric J Alm.

Water Research, 2022, https://doi.org/10.1016/j.watres.2022.118809

Making waves: wastewater surveillance of SARS-CoV-2 in an endemic future

Fuqing Wu†*, Wei Lin Lee†, Hongjie Chen†, Xiaoqiong Gu, Franciscus Chandra, Federica Armas, Amy Xiao, Mats Leifels, Steven F Rhode, Stefan Wuertz, Janelle Thompson, Eric J Alm*

Water Research, 2022, https://doi.org/10.1016/j.watres.2022.118535

Nationwide Trends in COVID-19 Cases and SARS-CoV‑2 RNA Wastewater Concentrations in the United States

Claire Duvallet*†, Fuqing Wu†, Kyle A. McElroy†, Maxim Imakaev†, Noriko Endo, Amy Xiao, Jianbo Zhang, Róisín Floyd-O’Sullivan, Morgan M. Powell, Samuel Mendola, Shane T. Wilson, Francis Cruz, Tamar Melman, Chaithra Lakshmi Sathyanarayana, Scott W. Olesen, Timothy B. Erickson, Newsha Ghaeli, Peter Chai, Eric J. Alm, Mariana Matus

ACS EST Water, 2022, https://doi.org/10.1021/acsestwater.1c00434.

Metrics to relate COVID-19 wastewater data to clinical testing dynamics

Amy Xiao†, Fuqing Wu†, Mary Bushman†, Jianbo Zhang, Maxim Imakaev, Peter R Chai, Claire Duvallet, Noriko Endo, Timothy B Erickson, Federica Armas, Brian Arnold, Hongjie Chen, Franciscus Chandra, Newsha Ghaeli, Xiaoqiong Gu, William P Hanage, Wei Lin Lee, Mariana Matus, Kyle A McElroy, Katya Moniz, Steven F Rhode, Janelle Thompson, Eric J Alm 

Water Research, 2022, https://doi.org/10.1016/j.watres.2022.118070.

SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases 

Fuqing Wu†, Amy Xiao†, Jianbo Zhang†, Katya Moniz, Noriko Endo, Federica Armas, Richard Bonneau, Megan A Brown, Mary Bushman, Peter R Chai, Claire Duvallet, Timothy B Erickson, Katelyn Foppe, Newsha Ghaeli, Xiaoqiong Gu, William P Hanage, Katherine H Huang, Wei Lin Lee, Mariana Matus, Kyle A McElroy, Jonathan Nagler, Steven F Rhode, Mauricio Santillana, Joshua A Tucker, Stefan Wuertz, Shijie Zhao, Janelle Thompson, Eric J Alm 

Science of The Total Environment, 2022, https://doi.org/10.1016/j.scitotenv.2021.150121. Posted online on July 06, 2020.

Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020

Fuqing Wu†, Amy Xiao†, Jianbo Zhang, Katya Moniz, Noriko Endo, Federica Armas, Mary Bushman, Peter R Chai, Claire Duvallet, Timothy B Erickson, Katelyn Foppe, Newsha Ghaeli, Xiaoqiong Gu, William P Hanage, Katherine H Huang, Wei Lin Lee, Kyle A McElroy, Steven F Rhode, Mariana Matus, Stefan Wuertz, Janelle Thompson, Eric J Alm

Water Research, 2021, https://doi.org/10.1016/j.watres.2021.117400.  Posted online on March 14, 2021.

Quantitative SARS-CoV-2 alpha variant B.1.1.7 tracking in wastewater by allele-specific RT-qPCR

Wei Lin Lee, Maxim Imakaev, Federica Armas, Kyle A McElroy, Xiaoqiong Gu, Claire Duvallet, Franciscus Chandra, Hongjie Chen, Mats Leifels, Samuel Mendola, Róisín Floyd-O’Sullivan, Morgan M Powell, Shane T Wilson, Karl LJ Berge, Claire YJ Lim, Fuqing Wu, Amy Xiao, Katya Moniz, Newsha Ghaeli, Mariana Matus, Janelle Thompson, Eric J Alm 

Environmental Science & Technology Letters, 2021, https://doi.org/10.1021/acs.estlett.1c00375.

Predictable control of RNA lifetime using engineered degradation-tuning RNAs

Qi Zhang, Duo Ma, Fuqing Wu, Kylie Standage-Beier, Xingwen Chen, Kaiyue Wu, Alexander A Green, Xiao Wang 

Nature chemical biology, 2021, https://doi.org/10.1038/s41589-021-00816-4.

SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases

Fuqing Wu, Jianbo Zhang, Amy Xiao, Xiaoqiong Gu, Wei Lin Lee, Federica Armas, Kathryn Kauffman, William Hanage, Mariana Matus, Newsha Ghaeli, Noriko Endo, Claire Duvallet, Mathilde Poyet, Katya Moniz, Alex D Washburne, Timothy B Erickson, Peter R Chai, Janelle Thompson, Eric J Alm 

mSystems, 2020, https://doi.org/10.1128/mSystems.00614-20. Posted online on April 07, 2020.

Design of Adjacent Transcriptional Regions to Tune Gene Expression and Facilitate Circuit Construction

Fuqing Wu†, Qi Zhang†, Xiao Wang 

Cell Systems, 2018, https://doi.org/10.1016/j.cels.2018.01.010.

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination

Fuqing Wu, Ri-Qi Su, Ying-Cheng Lai, Xiao Wang 

eLIFE, 2017, https://doi.org/10.7554/eLife.23702.

Build to understand: synthetic approaches to biology

Le-Zhi Wang, Fuqing Wu, Kevin Flores, Ying-Cheng Lai, Xiao Wang 

Integrative Biology, 2016, https://doi.org/10.1039/c5ib00252d.

Applications of synthetic gene networks

Fuqing Wu, Xiao Wang

Science Progress, 2015, https://doi.org/10.3184/003685015X1436880755.

Quorum-sensing crosstalk-driven synthetic circuits: from unimodality to trimodality

Fuqing Wu, David J Menn, Xiao Wang 

Chemistry & biology, 2014, https://doi.org/10.1016/j.chembiol.2014.10.008.

Live cell imaging fails to support viral-protein-mediated intercellular trafficking

Fuqing Wu, Jing Long, Shuai Wang, Junji Xing, Meili Li, Chunfu Zheng

 Archives of virology, 2012, 157, 1383-1386. 

Screening and identification of host factors interacting with UL14 of herpes simplex virus 1

Fuqing Wu, Junji Xing, Shuai Wang, Meili Li, Chunfu Zheng

Medical microbiology and immunology, 2012, 200, 203-208.

Characterization of nuclear import and export signals determining the subcellular localization of WD repeat-containing protein 42A (WDR42A)

Fuqing Wu, Shuai Wang, Junji Xing, Meili Li, Chunfu Zheng 

FEBS letters, 2012, 586, 1079-1085.

Granulysin production and anticryptococcal activity is dfependent upon a far upstream enhancer that binds STAT5 in human peripheral blood CD4+ T cells

Junji Xing†, Fuqing Wu†, Shuai Wang, Alan M Krensky, Christopher H Mody, Chunfu Zheng 

The Journal of Immunology, 2010, 185, 5074-5081. 

A Specific protein, flammutoxin expressed in the flammulina velutipes stipe

Meiling Zha, Fuqing Wu, Shu Wang, Mingjia Fu

CHINESE JOURNAL OF APPLIED & ENVIRONMENTAL BIOLOGY, 2010, 16, 738-740.

Molecular anatomy of subcellular localization of HSV-1 tegument protein US11 in living cells

Junji Xing, Fuqing Wu, Weiwei Pan, Chunfu Zheng

Virus research, 2010, 153, 71-81.