Article
Health Care Sciences & Services
Wan-Mui Chan, Jonathan Daniel Ip, Allen Wing-Ho Chu, Herman Tse, Anthony Raymond Tam, Xin Li, Mike Yat-Wah Kwan, Yat-Sun Yau, Wai-Shing Leung, Thomas Shiu-Hong Chik, Wing-Kin To, Anthony Chin-Ki Ng, Cyril Chik-Yan Yip, Rosana Wing-Shan Poon, Kwok-Hung Chan, Sally Cheuk-Ying Wong, Garnet Kwan-Yue Choi, David Christopher Lung, Vincent Chi-Chung Cheng, Ivan Fan-Ngai Hung, Kwok-Yung Yuen, Kelvin Kai-Wang To
Summary: The study revealed diverse SARS-CoV-2 genomes in imported infections and single lineages dominating local infections during the third and fourth waves in Hong Kong. Nonsynonymous mutations at the helicase gene were commonly found within the B.1.1.63 and B.1.36.27 lineages. Importantly, a single lineage with low-level local transmission played a key role in the fourth wave outbreak, possibly facilitated by a superspreading event or lower temperature in November.
LANCET REGIONAL HEALTH-WESTERN PACIFIC
(2021)
Article
Entomology
Yifang Ren, Huanhuan Lu, Longyan Chen, Simone Sabatelli, Chaojie Wang, Guanglin Xie, Ping Wang, Meike Liu, Wenkai Wang, Paolo Audisio
Summary: This study sequenced the mitogenomes of two species representing two tribes of Lamiinae, revealing their highly conservative nature, and reconstructed phylogenetic trees of Lamiinae based on mitogenomic data. The relationships between some tribes were explored, providing new insights into the evolution of Lamiinae.
Article
Multidisciplinary Sciences
Xue Cao, Wenjuan Li, Ting Wang, Dongzhi Ran, Veronica Davalos, Laura Planas-Serra, Aurora Pujol, Manel Esteller, Xiaolin Wang, Huichuan Yu
Summary: Epigenetic aging is associated with the risk of SARS-CoV-2 infection and developing severe COVID-19. The accumulation of epigenetic aging from COVID-19 may contribute to the post-COVID-19 syndrome among survivors.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Yuying Huang, Jing Li, Zerui Yang, Wenli An, Chunzhu Xie, Shanshan Liu, Xiasheng Zheng
Summary: The study analyzed the plastomes of ten Ficus species, revealing their similar genome structure but with variation in inverted repeat regions. The comparative analysis showed low sequence variability and suggested eight variable regions as potential molecular markers. Phylogenetic analysis grouped the species into three clades based on subgenera, supporting the Berg classification system. The study contributes to understanding genetic diversity and species evolution of Ficus, providing valuable information for taxonomic and phylogenetic studies.
Article
Entomology
Xian Zhou, Yuejie Lei, Christopher H. Dietrich, Min Huang
Summary: Typhlocybinae is the second-largest subfamily in the leafhopper family Cicadellidae, consisting of approximately 6000 species. The subfamily has been divided into six tribes, with Typhlocybini and Zyginellini being distinguished based on hind wing venation. However, there is a lack of mitogenome sequences representative of major lineages of Typhlocybini for phylogenetic analysis. In this study, complete mitogenome sequencing and functional annotations were performed for 19 Typhlocybinae species, and the results confirm the synonymy of Zyginellini with Typhlocybini while revealing the correspondence between certain generic groups and monophyletic lineages.
Article
Public, Environmental & Occupational Health
Tomas Nuno, Lidia Azurdia Sierra, Ada Wilkinson-Lee, Scott Carvajal, Jill de Zapien, Kiera Coulter, Carlos Figueroa, Mario Morales, Ramses Sepulveda, Refugio Sepulveda, Maia Ingram
Summary: Vaccine hesitancy poses a complex issue during the COVID-19 pandemic, particularly impacting Latinx rural, underserved, farmworker, disabled, and elderly populations. The Arizona Vaccine Confidence Network successfully increased vaccine uptake among priority populations through collaboration with key stakeholders and the use of community health workers as an intervention.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Immunology
Joy Sarojini Michael, Manigandan Venkatesan, Marilyn Mary Ninan, Dhanalakshmi Solaimalai, Lydia Jennifer Sumanth, Lalee Varghese, Regi Kurien, Rinku Polachirakkal Varghese, C. George Priya Doss
Summary: Whole genome sequencing analysis of Mucorales during and after the COVID-19 pandemic provides insight into the molecular epidemiology of these isolates in our community and establishes new mechanisms for intrinsic azole resistance.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Tina Fingesi, Lin Chung Yon, Sheila Soto, Cecilia Rosales
Summary: This study analyzed the perceptions, experiences, and impacts of COVID-19 among Arizona residents. The survey data showed unequal distribution of COVID-19 information sources between Southern and Central Arizona participants. There was also a significant difference in vaccination rates between the two regions. Women, especially Hispanic women, were more affected by job loss due to the pandemic.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Public, Environmental & Occupational Health
Collin J. Catalfamo, Kelly M. Heslin, Alexandra Shilen, Sana M. Khan, Josh R. Hunsaker, Erika Austhof, Leila Barraza, Felina M. Cordova-Marks, Leslie V. Farland, Pamela Garcia-Filion, Joshua Hoskinson, Megan Jehn, Lindsay N. Kohler, Karen Lutrick, Robin B. Harris, Zhao Chen, Yann C. Klimentidis, Melanie L. Bell, Kacey C. Ernst, Elizabeth T. Jacobs, Kristen Pogreba-Brown
Summary: This study aims to track the health status of diverse populations in Arizona and identify the long-term consequences of COVID-19 on health and well-being. With a scalable study design and collaborative infrastructure utilizing various recruitment sources and electronic data collection, the research is well-positioned to address the current and emerging issues associated with the pandemic.
FRONTIERS IN PUBLIC HEALTH
(2021)
Article
Plant Sciences
Zhongyu Zhou, Jing Wang, Tingting Pu, Jingjing Dong, Qin Guan, Jun Qian, Linchun Shi, Baozhong Duan
Summary: The complete chloroplast genomes of seven Isodon species were sequenced and analyzed, revealing potential molecular markers for identifying Isodon rubescens and its contaminants.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Mingyue Shang, Jiale Wang, Guona Dai, Jiamei Zheng, Binbin Liao, Jing Wang, Baozhong Duan
Summary: In this study, the chloroplast genomes of seven species from the Ajuga genus were sequenced and analyzed. The protein-coding genes were found to be reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Additionally, mutation hotspot regions were identified in the cp genomes, which could help distinguish different species and contaminants. Based on the analysis of the cp genomes and protein-coding genes, the position of Ajuga within the Lamiaceae family was confirmed, and the divergence time of Ajuga was estimated.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Immunology
Gavriella Hecht, Ariella P. Dale, Irene Ruberto, Guillermo Adame, Ryan Close, Sarah -Jean Snyder, Kathryn Pink, Nathanael Lemmon, Jessica Rudolfo, Michael Madsen, Andrea L. Wiens, Caitlin Cossaboom, Trevor Shoemaker, Mary J. Choi, Deborah Cannon, Inna Krapiunaya, Shannon Whitmer, Melissa Mobley, Emir Talundzic, John D. Klena, Heather Venkat
Summary: Two fatal cases of hantavirus infection were reported in Arizona, USA in 2020, with one person co-infected with SARS-CoV-2. Delayed identification of the cause of death resulted in a 9-month-long public health investigation after their deaths, complicating the identification of the vector or exposure.
EMERGING INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Faisal Nabi, Owais Ahmad, Yawar Ali Khan, Anas Nabi, Hashmi Md Amiruddin, Faizan Abul Qais, Aiman Masroor, Malik Hisamuddin, Vladimir N. Uversky, Rizwan Hasan Khan
Summary: The study screened FDA-approved drugs against SARS-CoV-2 proteins and found potential interactions with anticancer, antipsychotic, and antiviral drugs. Molecular dynamics simulations revealed protein evolution upon drug interaction, and a phylogenetic analysis was conducted on 43 coronavirus strains infecting 12 mammalian species.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Public, Environmental & Occupational Health
Velia Leybas Nuno, Namoonga M. Mantina, Oriyomi Dawodu, Maureen Dykinga, Dametreea L. Carr, Kristen Pogreba-Brown, Felina Cordova-Marks, Megan Jehn, Kimberly Peace-Tuskey, Leila Barraza, Pamela Garcia-Filion
Summary: This study aims to understand the impact of COVID-19 on adolescents aged 12-17 in Arizona and utilizes Intersectionality Theory to consider their diverse identities and social context. Data is collected through online surveys and the study is designed to span over 5 years.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Virology
Shizheng Qiu, Keyang Zheng, Yang Hu, Guiyou Liu
Summary: Observational studies have shown that vitamin D supplementation reduces the risk of COVID-19 infection. This study investigated the genetic correlation and causal relationship between genetically determined vitamin D and COVID-19, and identified overlapping susceptibility loci. The results indicated that genetically determined vitamin D is associated with COVID-19, and increased serum 25 hydroxyvitamin D concentration may benefit the prevention and treatment of COVID-19.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Biochemical Research Methods
Nicholas A. Bokulich, Pawel Laniewski, Anja Adamov, Dana M. Chase, J. Gregory Caporaso, Melissa M. Herbst-Kralovetz
Summary: This study provides insights into the interactions between vaginal microbiome, metabolome, and genital inflammation in cervical neoplasms. The integration of multi-omics data reveals the characteristic features and predictive models of the cervicovaginal microenvironment. These findings highlight the importance of multi-omics approaches in microbiome research and the potential contribution of host-microbe interactions to cervical carcinogenesis.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Medicine, General & Internal
Brooke L. Deatherage Kaiser, Dawn N. Birdsell, Janine R. Hutchison, Johanna Thelaus, Sarah C. Jenson, Voahangy Andrianaivoarimanana, Mona Bystroem, Kerstin Myrtennaes, Ryelan F. McDonough, Roxanne D. Nottingham, Jason W. Sahl, Herbert P. Schweizer, Minoarisoa Rajerison, Mats Forsman, David S. Wunschel, David M. Wagner
Summary: Antimicrobial resistance is a growing concern, and we studied the proteins associated with Yersinia pestis and Francisella tularensis strains to identify potential protein signatures for antimicrobial resistance (AMR). We found that protein expression was significantly influenced by AMR, even in the absence of antibiotics in growth media. Additionally, the abundance of specific proteins involved in metabolic pathways and biological functions was altered in AMR strains, regardless of species or resistance mechanism. These features could be used to develop novel approaches for identifying AMR phenotypes.
FRONTIERS IN MEDICINE
(2022)
Article
Infectious Diseases
Nathan E. Stone, Carina M. Hall, Marielisa Ortiz, Shelby M. Hutton, Ella Santana-Propper, Kimberly R. Celona, Charles H. D. Williamson, Nicole Bratsch, Luis G. V. Fernandes, Joseph D. Busch, Talima Pearson, Sarai Rivera-Garcia, Fred Soltero, Renee Galloway, Jason W. Sahl, Jarlath E. Nally, David M. Wagner
Summary: This study investigated the diversity and distribution of Leptospira bacteria in the environment in Puerto Rico. The results showed that diverse and pathogenic Leptospira were abundant and widespread, with some lineages persisting in soil for over a year. This research will contribute to improving the monitoring and diagnosis of leptospirosis.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Article
Immunology
Lisa J. Speiser, Sabirah Kasule, Carina M. Hall, Jason W. Sahl, David M. Wagner, Chris Saling, Amy Kole, Andrew J. Meltzer, Victor Davila, Robert Orenstein, Thomas Grys, Erin Graf
Summary: Melioidosis, caused by Burkholderia pseudomallei, is a highly lethal infection with a particularly high fatality rate if left untreated or undiagnosed. It is endemic to Asia, Australia, South America, and the Caribbean, but the number of cases reported in the United States is increasing. This study highlights the rare occurrence of melioidosis presenting as a mycotic aneurysm in the United States and emphasizes the need for diagnostic awareness and epidemiological concerns.
OPEN FORUM INFECTIOUS DISEASES
(2022)
Article
Veterinary Sciences
Camila Hamond, Karen LeCount, Ellie J. Putz, Darrell O. Bayles, Patrick Camp, Marga G. A. Goris, Hans van der Linden, Nathan E. Stone, Linda K. Schlater, Jason W. Sahl, David M. Wagner, Jarlath E. Nally
Summary: This study reports the isolation of L. borgpetersenii serovar Tarassovi from the urine of a dairy cow in the U.S. for the first time. The isolate was characterized using whole-genome sequencing, serotyping, MALDI, and immunoblotting. This finding highlights the importance of culture, genotyping, and serotyping for accurate classification of leptospires and the design of effective vaccine and diagnostic strategies.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Multidisciplinary Sciences
Carina M. Hall, Daniel Romero-Alvarez, Madison Martz, Ella Santana-Propper, Lora Versluis, Laura Jimenez, Abdelghafar Alkishe, Joseph D. Busch, Trevor Maness, Jonathan Stewart, Tom Sidwa, Jay E. Gee, Mindy G. Elrod, Zachary Weiner, Alex R. Hoffmaster, Jason W. Sahl, Johanna S. Salzer, A. Townsend Peterson, Amanda Kieffer, David M. Wagner
Summary: The study found that the risk of acquiring melioidosis from the environment in the continental U.S. is low, even at locations where locally acquired cases have occurred.
Article
Cell Biology
Evan A. Elko, Georgia A. Nelson, Heather L. Mead, Erin J. Kelley, Sophia T. Carvalho, Nathan G. Sarbo, Caroline E. Harms, Virginia Le Verche, Angelo A. Cardoso, Jennifer L. Ely, Annalee S. Boyle, Alejandra Pina, Sierra N. Henson, Fatima Rahee, Paul S. Keim, Kimberly R. Celona, Jinhee Yi, Erik W. Settles, Daniela A. Bota, George C. Yu, Sheldon R. Morris, John A. Zaia, Jason T. Ladner, John A. Altin
Summary: The COVID-19 pandemic has led to widespread vaccination campaigns against coronaviruses. This study investigates the immune response to the mRNA-1273 vaccine and its effect on previously encountered coronaviruses. The results show that the vaccine induces antibody responses against a range of coronaviruses and provides insights into the formation of broad reactivity antibodies.
Article
Biochemistry & Molecular Biology
Jason T. Ladner, Jonathan M. Palmer, Cassandra L. Ettinger, Jason E. Stajich, Terence M. Farrell, Brad M. Glorioso, Becki Lawson, Steven J. Price, Anne G. Stengle, Daniel A. Grear, Jeffrey M. Lorch
Summary: Through analyzing the genomes of Ophidiomyces ophiodiicola (Oo) strains, it was found that strains in the eastern United States formed a distinct clade from European strains. Molecular dating suggests that the divergence between these clades occurred too recently for Oo to have dispersed between continents through snake movements. The lack of intermediate nonrecombinant strains between clonal lineages in the United States indicates that Oo has been introduced multiple times from an unsampled source population, with several introductions happening in the last few hundred years. Additionally, the most common clonal lineages in the United States have recently expanded.
Article
Biochemical Research Methods
Michal Ziemski, Anja Adamov, Lina Kim, Lena Floerl, Nicholas A. Bokulich
Summary: This study aims to address the issues of reproducible reuse and management of public nucleotide sequence data. The developed q2-fondue software package provides programmatic access and management of NCBI SRA data, integrates with the QIIME 2 ecosystem, and mitigates the risk of data loss. Demonstrations showcased its versatility and capabilities.
Article
Microbiology
Alexa Schuettenberg, Alejandra Pina, Morgan Metrailer, Ronald Guillermo Pelaez-Sanchez, Piedad Agudelo-Florez, Juan Alvaro Lopez, Luke Ryle, Fernando P. Monroy, John A. Altin, Jason T. Ladner
Summary: Emerging infectious diseases pose a serious threat to human beings, and understanding the diversity and ecology of viruses in the animal virosphere can predict the appearance of emerging viruses. High-throughput metagenomic sequencing accelerates virus discovery, and serological assays can complement the understanding of virus circulation. By evaluating the application of immunoglobulin-binding proteins in nonhuman mammals, we can better understand the distribution and prevalence of viruses that could spill over into humans.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemical Research Methods
Sierra N. Henson, Evan A. Elko, Piotr M. Swiderski, Yong Liang, Anna L. Engelbrektson, Alejandra Pina, Annalee S. Boyle, Zane Fink, Salvatore J. Facista, Vidal Martinez, Fatima Rahee, Annabelle Brown, Erin J. Kelley, Georgia A. Nelson, Isaiah Raspet, Heather L. Mead, John A. Altin, Jason T. Ladner
Summary: PepSeq is an in vitro platform for highly multiplexed proteomic assays using DNA-barcoded peptides. It allows for fast and cost-effective epitope-level analysis of antibody reactivity. The protocol involves DNA design, peptide synthesis, binding, sequencing, and data analysis.
Article
Microbiology
Carina M. M. Hall, Nawarat Somprasong, Johannah P. P. Hagen, Roxanne Nottingham, Jason W. W. Sahl, Jessica R. R. Webb, Mark Mayo, Bart J. J. Currie, Yuwana Podin, David M. M. Wagner, Paul Keim, Herbert P. P. Schweizer
Summary: Cefiderocol is a siderophore cephalosporin designed for treating infections caused by beta-lactam and multidrug-resistant Gram-negative bacteria. Resistance in clinical B. pseudomallei isolates from Australia is caused by an uncharacterized mechanism. The PiuA outer membrane receptor plays a major role in cefiderocol nonsusceptibility in isolates from Malaysia.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Erin J. Kelley, Sierra N. Henson, Fatima Rahee, Annalee S. Boyle, Anna L. Engelbrektson, Georgia A. Nelson, Heather L. Mead, N. Leigh Anderson, Morteza Razavi, Richard Yip, Jason T. Ladner, Thomas J. Scriba, John A. Altin
Summary: Current methods for detecting infections are limited in their ability to query multiple agents and provide immune response information. In this study, the authors use a novel approach to monitor infection events in the human virome by analyzing temporally coordinated changes in highly-multiplexed antibody measurements from longitudinal blood samples. They identify over 650 events across 48 virus species and observe strong epidemic effects. This approach provides a high-resolution view of viral/host dynamics and has implications for immunology and epidemiology research.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Jolene R. Bowers, Hayley D. Yaglom, Crystal M. Hepp, Ashlyn Pfeiffer, Daniel Jasso-Selles, Nicole Bratsch, J. T. Nashio, Megan Folkerts, Sara M. Wilbur, Chris French, Darrin Lemmer, Kathryn Fitzpatrick, Trung Huynh, Kenneth Komatsu, James B. McAuley, Ryan Close, David M. Engelthaler
Summary: This article discusses the introduction and spread of two unique viral lineages of SARS-CoV-2 within the White Mountain Apache Tribe in Arizona. Both genomic sequencing and traditional epidemiological strategies (e.g., contract tracing) were used to understand the nature of the spread of both lineages. Beyond providing a robust genomic analysis of the epidemiology of the outbreaks, this work also highlights the successful efforts of the local public health response.
Article
Biochemistry & Molecular Biology
Jason T. Ladner, Jason W. Sahl
Summary: Pathogen genome sequencing has become a routine part of outbreak response and epidemic preparedness. This Essay discusses the innovations enabling routine pathogen genome sequencing, the use of genome sequences to understand and control infectious disease spread, and the impact of the SARS-CoV-2 pandemic on pathogen genomics. The challenges in improving the utility of pathogen genome sequencing in the future are also outlined.