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original article |
Date |
Title |
Authors Max. 6 Authors |
| 1 |
[GO] |
2026―May―29 |
Genomic analysis of Vibrio cholerae in Western Kenya (2015-2023) reveals persistence of pandemic ST69 and presence of the European-associated ST8 lineage |
Erick C Kipkirui, Vanessa Natasha, Collins Kigen, James W Muturi, Ronald K Kirera, Margaret C Koech, Mary C Kirui, Nancy C Kipkemoi, Janet N Ndonye, Sheilla Jerotich, Luis Pow Sang, Lillian Musila, Elizabeth A Odundo |
| 2 |
[GO] |
2026―Feb―24 |
Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes |
Paweł Błażej, Dorota Mackiewicz, Paweł Mackiewicz |
| 3 |
[GO] |
2026―Feb―14 |
The genomic diversity of SARS-CoV-2 Omicron lineages collected during routine sentinel surveillance in Tanzania between November 2022 and July 2023 |
Lawrence Amon Mapunda, Maria Ezekiely Kelly, Shimba Henerico, Monica Francis, Azizi Ituka, Omega Machange, Adela Kisanga, Jackson Peter Mushumbusi, Ferdinand Ndunguru, Ibrahim Ireneus Mauki, Olympia Godbless Machange, Robert Baluhya, Japhet Msuya, Ramdhani Libenanga, Ambele Mwafulango, Peter Van Heusden, Seth Inzaule, Gerald Misinzo, Nyambura Moremi |
| 4 |
[GO] |
2025―Oct―21 |
Natural selection exerted by historical coronavirus epidemic(s): comparative genetic analysis in China Kadoorie Biobank and UK Biobank |
Sam Morris, Kuang Lin, Iona Y. Millwood, Canqing Yu, Jun Lv, Pei Pei, Liming Li, Dianjianyi Sun, George Davey Smith, Zhengming Chen, Robin G. Walters |
| 5 |
[GO] |
2025―Oct―14 |
Genomic diversity and surveillance of SARS-CoV-2 in Nigeria |
Thomas J. Y. Kono, Ezenwa J. Onyemata, Natalia Blanco, Chika K. Onwuamah, Nnaemeka Ndodo, Paul Oluniyi, Olanrewaju Lawal, Christina Riley, Sophia Osawe, Cheryl Baxter, Anna Winters, Chenfeng Xiong, Christian T. Happi, Babatunde L. Salako, Ifedayo Adetifa, Alash’le Abimiku, Manhattan Charurat, Kristen A. Stafford, Timothy O’Connor, Meagan Fitzpatrick, Mohammad M. Sajadi, Patrick Dakum, Fati Murtala-Ibrahim, Nifarta Andrew, Aminu Musa, Tolulope Adenekan, Kenneth Ewerem, Victoria Etuk, Mmedorenyin Okon, Weiyu Luo, Xin Wu, Tulio de Oliveira, Eduan Wilkinson, Houriiyah Tegally, Jenicca Poongavanan, Michelle Parker, Danilo Silva, Joicymara S. Xavier, Vivek Naranbhai, Salim A. Karim, Kennedy Otwombe |
| 6 |
[GO] |
2025―Sep―26 |
Complete genome sequence analysis of Sarbecovirus (severe acute respiratory syndrome-related coronaviruses) from Zimbabwean insectivorous bats |
Vimbiso Chidoti, Anaïs Loisier, Taona Zinyakasa, Mathieu Bourgarel, Valérie Pinarello, Gift Matope, Ngoni Chiweshe, Dorothée Missé, Ellen Mwandiringana, Hélène De Nys, Florian Liégeois |
| 7 |
[GO] |
2025―Aug―28 |
Peripheral transcriptional responses to experimental SARS-CoV-2 inoculation in North American elk cows and calves |
Bruna Petry, Kaitlyn M. Sarlo Davila, Alexandra C. Buckley, Eric D. Cassmann, Steven. C. Olsen, Paola M. Boggiatto, Mitchell V. Palmer, Ellie J. Putz |
| 8 |
[GO] |
2025―Mar―21 |
Altered structural and transporter-related gene expression patterns in the placenta play a role in fetal demise during Porcine reproductive and respiratory syndrome virus infection |
Angelica Van Goor, Alex Pasternak, Kristen E. Walker, Shannon Chick, John C. S. Harding, Joan K. Lunney |
| 9 |
[GO] |
2025―Mar―21 |
Seminal plasma proteomics of asymptomatic COVID-19 patients reveals disruption of male reproductive function |
Jialyu Huang, Yufang Su, Jiawei Wang, Zheng Fang, Yiwei Zhang, Hong Chen, Xinxia Wan, Yuanhuan Xiong, Ning Song, Houyang Chen, Xingwu Wu |
| 10 |
[GO] |
2025―Jan―29 |
Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencing |
Ignacio Garcia, Rasmus K. Riis, Line V. Moen, Andreas Rohringer, Elisabeth H. Madslien, Karoline Bragstad |
| 11 |
[GO] |
2024―Dec―30 |
Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses |
Xiaoyu Guo, Zhenming Wu, Shu Zhang, Jin Zhao |
| 12 |
[GO] |
2024―Nov―11 |
Sustained applicability of SARS-CoV-2 variants identification by Sanger Sequencing Strategy on emerging various SARS-CoV-2 Omicron variants in Hiroshima, Japan |
Chanroth Chhoung, Ko Ko, Serge Ouoba, Zayar Phyo, Golda Ataa Akuffo, Aya Sugiyama, Tomoyuki Akita, Hiroshi Sasaki, Tadashi Yamamoto, Kazuaki Takahashi, Junko Tanaka |
| 13 |
[GO] |
2024―Oct―21 |
Comparison of genotypic features between two groups of antibiotic resistant Klebsiella pneumoniae clinical isolates obtained before and after the COVID-19 pandemic from Egypt |
Pansee Gamaleldin, Mustafa Alseqely, Benjamin A. Evans, Hoda Omar, Alaa Abouelfetouh |
| 14 |
[GO] |
2024―Oct―21 |
Fine-tuning of a CRISPRi screen in the seventh pandemic Vibrio cholerae |
Kevin Debatisse, Théophile Niault, Sarah Peeters, Amandine Maire, Busra Toktas, Baptiste Darracq, Zeynep Baharoglu, David Bikard, Didier Mazel, Céline Loot |
| 15 |
[GO] |
2024―Jun―28 |
UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example |
Alexander Thomas, Thomas Battenfeld, Ivana Kraiselburd, Olympia Anastasiou, Ulf Dittmer, Ann-Kathrin Dörr, Adrian Dörr, Carina Elsner, Jule Gosch, Vu Thuy Khanh Le-Trilling, Simon Magin, René Scholtysik, Pelin Yilmaz, Mirko Trilling, Lara Schöler, Johannes Köster, Folker Meyer |
| 16 |
[GO] |
2024―May―16 |
Genomic analysis of severe COVID-19 considering or not asthma comorbidity: GWAS insights from the BQC19 cohort |
Omayma Amri, Anne-Marie Madore, Anne-Marie Boucher-Lafleur, Catherine Laprise |
| 17 |
[GO] |
2024―May―01 |
Ocular A-to-I RNA editing signatures associated with SARS-CoV-2 infection |
Yun-Yun Jin, Ya-Ping Liang, Wen-Hao Huang, Liang Guo, Li-Li Cheng, Tian-Tian Ran, Jin-Ping Yao, Lin Zhu, Jian-Huan Chen |
| 18 |
[GO] |
2024―Apr―17 |
Comprehensive genomic analysis of the SARS-CoV-2 Omicron variant BA.2.76 in Jining City, China, 2022 |
Qiang Yin, Wei Liu, Yajuan Jiang, Qiang Feng, Xiaoyu Wang, Huixin Dou, Zanzan Liu, Feifei He, Yingying Fan, Baihai Jiao, Boyan Jiao |
| 19 |
[GO] |
2024―Mar―12 |
Decoding HiPSC-CM’s Response to SARS-CoV-2: mapping the molecular landscape of cardiac injury |
Sicheng Chen, Zhenquan Fu, Kaitong Chen, Xinyao Zheng, Zhenyang Fu |
| 20 |
[GO] |
2024―Jan―13 |
Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater |
Michael J. Conway, Hannah Yang, Lauren A. Revord, Michael P. Novay, Rachel J. Lee, Avery S. Ward, Jackson D. Abel, Maggie R. Williams, Rebecca L. Uzarski, Elizabeth W. Alm |
| 21 |
[GO] |
2023―Oct―18 |
Potential network markers and signaling pathways for B cells of COVID-19 based on single-cell condition-specific networks |
Ying Li, Liqin Han, Peiluan Li, Jing Ge, Yun Xue, Luonan Chen |
| 22 |
[GO] |
2023―Jul―10 |
The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection |
Anastassia Bykova, Andreu Saura, Galina V. Glazko, Abiel Roche-Lima, Vyacheslav Yurchenko, Igor B. Rogozin |
| 23 |
[GO] |
2023―Jun―12 |
Integrative multi-omics approach for identifying molecular signatures and pathways and deriving and validating molecular scores for COVID-19 severity and status |
Danika Lipman, Sandra E. Safo, Thierry Chekouo |
| 24 |
[GO] |
2023―Jun―10 |
Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022 |
Cassien Nduwimana, Néhémie Nzoyikorera, Armstrong Ndihokubwayo, Théogène Ihorimbere, Célestin Nibogora, Adolphe Ndoreraho, Oscar Hajayandi, Jean Claude Bizimana, Idrissa Diawara, Dionis Niyonizigiye, Joseph Nyandwi |
| 25 |
[GO] |
2023―May―18 |
A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes |
Saeedeh Akbari Rokn Abadi, Amirhossein Mohammadi, Somayyeh Koohi |
| 26 |
[GO] |
2023―Jan―10 |
Evaluation and limitations of different approaches among COVID-19 fatal cases using whole-exome sequencing data |
Natalia Forgacova, Zuzana Holesova, Rastislav Hekel, Tatiana Sedlackova, Zuzana Pos, Lucia Krivosikova, Pavol Janega, Kristina Mikus Kuracinova, Pavel Babal, Peter Radvak, Jan Radvanszky, Juraj Gazdarica, Jaroslav Budis, Tomas Szemes |
| 27 |
[GO] |
2023―Jan―05 |
Correction: A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones |
Filippo Utro, Chaya Levovitz, Kahn Rhrissorrakrai, Laxmi Parida |
| 28 |
[GO] |
2022―Nov―17 |
A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2 |
Swati Gupta, Amit Kumar, Nivedita Gupta, Deepak R. Bharti, Neeraj Aggarwal, Vasanthapuram Ravi |
| 29 |
[GO] |
2022―Oct―18 |
Cov2clusters: genomic clustering of SARS-CoV-2 sequences |
Benjamin Sobkowiak, Kimia Kamelian, James E. A. Zlosnik, John Tyson, Anders Gonçalves da Silva, Linda M. N. Hoang, Natalie Prystajecky, Caroline Colijn |
| 30 |
[GO] |
2022―Sep―01 |
Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya |
Josiah O. Kuja, Bernard N. Kanoi, Renzo F. Balboa, Clement Shiluli, Michael Maina, Harrison Waweru, Kimita Gathii, Mary Mungai, Moses Masika, Omu Anzala, Matilu Mwau, Taane G. Clark, John Waitumbi, Jesse Gitaka |
| 31 |
[GO] |
2022―Jul―15 |
Genomic surveillance of SARS-CoV-2 in US military compounds in Afghanistan reveals multiple introductions and outbreaks of Alpha and Delta variants |
Irina Maljkovic Berry, Jun Hang, Christian Fung, Yu Yang, Marcus Chibucos, Adam Pollio, Jay Gandhi, Tao Li, Matthew A. Conte, Grace M. Lidl, Jay A. Johannigman, Heather Friberg |
| 32 |
[GO] |
2022―Jul―14 |
Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina |
Nadia B. Olivero, Ana S. Gonzalez-Reiche, Viviana E. Re, Gonzalo M. Castro, María B. Pisano, Paola Sicilia, María G. Barbas, Zenab Khan, Adriana van de Guchte, Jayeeta Dutta, Paulo R. Cortes, Mirelys Hernandez-Morfa, Victoria E. Zappia, Lucia Ortiz, Ginger Geiger, Daniela Rajao, Daniel R. Perez, Harm van Bakel, Jose Echenique |
| 33 |
[GO] |
2022―Jun―03 |
SARS-CoV-2 Delta variant isolates from vaccinated individuals |
Lauren Brinkac, Sheila Diepold, Shane Mitchell, Stephanie Sarnese, Lee F. Kolakowski, William M. Nelson, Katharine Jennings |
| 34 |
[GO] |
2022―May―30 |
A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus |
Klaudia Chrzastek, Chandana Tennakoon, Dagmara Bialy, Graham Freimanis, John Flannery, Holly Shelton |
| 35 |
[GO] |
2022―Apr―22 |
Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq |
Derek Tshiabuila, Jennifer Giandhari, Sureshnee Pillay, Upasana Ramphal, Yajna Ramphal, Arisha Maharaj, Ugochukwu Jacob Anyaneji, Yeshnee Naidoo, Houriiyah Tegally, Emmanuel James San, Eduan Wilkinson, Richard J. Lessells, Tulio de Oliveira |
| 36 |
[GO] |
2022―Apr―11 |
DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 |
Alexander Yermanos, Kai-Lin Hong, Andreas Agrafiotis, Jiami Han, Sarah Nadeau, Cecilia Valenzuela, Asli Azizoglu, Roy Ehling, Beichen Gao, Michael Spahr, Daniel Neumeier, Ching-Hsiang Chang, Andreas Dounas, Ezequiel Petrillo, Ina Nissen, Elodie Burcklen, Mirjam Feldkamp, Christian Beisel, Annette Oxenius, Miodrag Savic, Tanja Stadler, Fabian Rudolf, Sai T. Reddy |
| 37 |
[GO] |
2022―Apr―04 |
Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA |
Longhua Guo, James Boocock, Evann E. Hilt, Sukantha Chandrasekaran, Yi Zhang, Chetan Munugala, Laila Sathe, Noah Alexander, Valerie A. Arboleda, Jonathan Flint, Eleazar Eskin, Chongyuan Luo, Shangxin Yang, Omai B. Garner, Yi Yin, Joshua S. Bloom, Leonid Kruglyak |
| 38 |
[GO] |
2022―Feb―11 |
Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences |
Áine O’Toole, Oliver G. Pybus, Michael E. Abram, Elizabeth J. Kelly, Andrew Rambaut |
| 39 |
[GO] |
2021―Nov―17 |
A common methodological phylogenomics framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones |
Filippo Utro, Chaya Levovitz, Kahn Rhrissorrakrai, Laxmi Parida |
| 40 |
[GO] |
2021―Oct―30 |
SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels |
Adriano Di Pasquale, Nicolas Radomski, Iolanda Mangone, Paolo Calistri, Alessio Lorusso, Cesare Cammà |
| 41 |
[GO] |
2021―Jul―14 |
Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa |
Wasfi Fares, Anissa Chouikha, Kais Ghedira, Meriam Gdoura, Dorra Rezig, Sondes Haddad Boubaker, Imen Ben Dhifallah, Henda Touzi, Walid Hammami, Zina Meddeb, Amel Sadraoui, Nahed Hogga, Imen Abouda, Aurélia Kwasiborski, Véronique Hourdel, Guillain Mikaty, Valérie Caro, Jean-Claude Manuguerra, Nissaf Ben Alaya, Henda Triki |
| 42 |
[GO] |
2021―May―20 |
Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil |
Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Amanda de Menezes Mayer, Gabriela Bettella Cybis, Carla Andretta Moreira Neves, Patrícia Aline Gröhs Ferrareze, Meriane Demoliner, Paula Rodrigues de Almeida, Juliana Schons Gularte, Alana Witt Hansen, Matheus Nunes Weber, Juliane Deise Fleck, Ricardo Ariel Zimerman, Lívia Kmetzsch, Fernando Rosado Spilki, Claudia Elizabeth Thompson |
| 43 |
[GO] |
2021―May―17 |
Population genetic considerations for using biobanks as international resources in the pandemic era and beyond |
Hannah Carress, Daniel John Lawson, Eran Elhaik |
| 44 |
[GO] |
2021―Mar―12 |
Unveiling the long non-coding RNA profile of porcine reproductive and respiratory syndrome virus-infected porcine alveolar macrophages |
Junxin Gao, Yu Pan, Yunfei Xu, Wenli Zhang, Lin Zhang, Xi Li, Zhijun Tian, Hongyan Chen, Yue Wang |
| 45 |
[GO] |
2021―Feb―18 |
SARS-CoV-2 early infection signature identified potential key infection mechanisms and drug targets |
Yue Li, Ashley Duche, Michael R. Sayer, Don Roosan, Farid G. Khalafalla, Rennolds S. Ostrom, Jennifer Totonchy, Moom R. Roosan |
| 46 |
[GO] |
2021―Jan―20 |
Identification and analysis of long non-coding RNAs and mRNAs in chicken macrophages infected with avian infectious bronchitis coronavirus |
Hao Li, Pengfei Cui, Xue Fu, Lan Zhang, Wenjun Yan, Yaru Zhai, Changwei Lei, Hongning Wang, Xin Yang |
| 47 |
[GO] |
2020―Dec―04 |
A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2 |
Daryl M. Gohl, John Garbe, Patrick Grady, Jerry Daniel, Ray H. B. Watson, Benjamin Auch, Andrew Nelson, Sophia Yohe, Kenneth B. Beckman |
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