Article
Multidisciplinary Sciences
Lyora A. Cohen-Aharonov, Annie Rebibo-Sabbah, Adar Yaacov, Roy Z. Granit, Merav Strauss, Raul Colodner, Ori Cheshin, Shai Rosenberg, Ronen Eavri
Summary: In this study, the researchers proposed a solution for large-scale viral screening and specific variant analysis by integrating DNA barcoding technology, sample pooling, and Next Generation Sequencing (NGS) methods. The solution allows high throughput testing with high sensitivity and specificity, and enables variant analysis at a single nucleotide resolution.
News Item
Multidisciplinary Sciences
Heidi Ledford
Summary: Despite a decrease in SARS-CoV-2 infections in some nations, there is still concern about when the next wave of the pandemic will hit and what form it will take.
Editorial Material
Multidisciplinary Sciences
Ewen Callaway
Summary: New technologies may offer stronger or wider immunity, but they will face competition for market share.
Review
Microbiology
Jessica A. Plante, Brooke M. Mitchell, Kenneth S. Plante, Kari Debbink, Scott C. Weaver, Vineet D. Menachery
Summary: Despite the development of vaccines, COVID-19 caused by SARS-CoV-2 continues to be a global concern due to the emergence of new variants, raising worries about increased spread and potential impacts on immunity.
CELL HOST & MICROBE
(2021)
Article
Biochemistry & Molecular Biology
Yu-Chieh Liao, Feng-Jui Chen, Min-Chieh Chuang, Han-Chieh Wu, Wan-Chen Ji, Guann-Yi Yu, Tsi-Shu Huang
Summary: The widely used amplicon-based approach for SARS-CoV-2 genome sequencing has limitations, including low sequence coverage and high resource requirements. To address these issues, the researchers proposed a single PCR method to efficiently detect spike gene mutations and developed a bioinformatic protocol for accurate variant calling of spike protein. Their approach showed high detection rates and robustness against different sequencing datasets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Virology
David Brandt, Marina Simunovic, Tobias Busche, Markus Haak, Peter Belmann, Sebastian Juenemann, Tizian Schulz, Levin Joe Klages, Svenja Vinke, Michael Beckstette, Ehmke Pohl, Christiane Scherer, Alexander Sczyrba, Joern Kalinowski
Summary: Genomic surveillance of the SARS-CoV-2 pandemic is crucial and achieved mainly through amplicon sequencing protocols. A significant deletion in the ORF8 gene has been discovered, indicating a mutation hotspot, with many deletions not identified in standard data analysis.
Article
Multidisciplinary Sciences
Sk Sarif Hassan, Vaishnavi Kodakandla, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Tarek Mohamed Abd El-Aziz, Kazuo Takayama, Ramesh Kandimalla, Amos Lal, Angel Serrano-Aroca, Gajendra Kumar Azad, Alaa A. A. Aljabali, Giorgio Palu, Gaurav Chauhan, Parise Adadi, Murtaza Tambuwala, Adam M. Brufsky, Wagner Baetas-da-Cruz, Debmalya Barh, Vasco Azevedo, Nikolas G. Bazan, Bruno Silva Andrade, Raner Jose Santana Silva, Vladimir N. Uversky
Summary: Accessory protein ORF8 in SARS-CoV-2 shows high variability and can inhibit antigen presentation, aiding the virus in evading immunity and replicating. The Q27STOP mutation defines a new lineage and contributes to the second wave of COVID-19. Multiple ORF8 protein variants were identified, with 9 possible unique variants showing significant features.
Article
Genetics & Heredity
Lavanya Singh, James E. San, Houriiyah Tegally, Pius M. Brzoska, Ugochukwu J. Anyaneji, Eduan Wilkinson, Lindsay Clark, Jennifer Giandhari, Sureshnee Pillay, Richard J. Lessells, Darren Patrick Martin, Manohar Furtado, Anmol M. Kiran, Tulio de Oliveira
Summary: This study presents a method to improve the quality of whole-genome assemblies using Sanger sequencing. By amplifying key genomic regions with custom primers and sequencing them using a Sanger sequencing wet-laboratory protocol, the authors were able to obtain high-quality consensus sequences. The method was successful in confirming key mutations in the spike (S) protein in a high percentage of samples.
MICROBIAL GENOMICS
(2022)
Article
Virology
Pia Laine, Hanna Nihtila, Ella Mustanoja, Annina Lyyski, Anne Ylinen, Jukka Hurme, Lars Paulin, Sakari Jokiranta, Petri Auvinen, Taru Meri
Summary: While most spontaneous mutations in the viral genome have no consequences, some can affect diagnostic tests. A variant strain found in Southern Finland in February 2021 showed mutations in the N gene that led to negative results in PCR tests. This variant belongs to the B.1.1.318 Pango lineage and differs from the Beta variant in certain aspects.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Review
Immunology
Xiaomin Chen, Yutong Kang, Jing Luo, Kun Pang, Xin Xu, Jinyu Wu, Xiaokun Li, Shengwei Jin
Summary: The ongoing COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has highlighted the importance of next-generation sequencing in understanding the virus. NGS analysis has provided insights into the origin and transmission of SARS-CoV-2, as well as related factors like ACE2 expression levels, gut microbiota dysbiosis, and immunogenetics of patients. These sequencing techniques have the potential to identify new hosts, aid in diagnostic development, and discover therapeutic targets, offering crucial support in the fight against future public health emergencies.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Immunology
Haijun Wang, Zili Zhang, Junfen Zhou, Shuqing Han, Zhenyu Kang, Haoyu Chuang, Heng Fan, Hongyang Zhao, Lin Wang, Yunjia Ning, Alexey Sarapultsev, Willis X. Li, Jinghong Li, Zhicheng Lin, Shanshan Luo, Nian Xiong, Desheng Hu
Summary: This study reported a case series of 8 COVID-19 patients with prominent new-onset neurological manifestations. Detection rate of SARS-CoV-2 in CSF was high and proteomic alterations in CSF showed high specificity in neurological infections.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biochemical Research Methods
Matteo Chiara, Anna Maria D'Erchia, Carmela Gissi, Caterina Manzari, Antonio Parisi, Nicoletta Resta, Federico Zambelli, Ernesto Picardi, Giulio Pavesi, David S. Horner, Graziano Pesole
Summary: Various NGS-based strategies have been used to trace infectious agent origins and develop molecular diagnostic tests. The ongoing COVID-19 pandemic has caused severe societal and economic costs, emphasizing the importance of efficient sequencing methods. However, different technologies and approaches have their own advantages and limitations, highlighting the need for better integration and sharing of data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Scott Burkholz, Michael Rubsamen, Luke Blankenberg, Richard T. Carback III, Daria Mochly-Rosen, Paul E. Harris
Summary: Analysis of next-generation sequencing data linked with clinical metadata reveals that Omicron reinfections occur at a higher frequency and within a shorter time interval compared to pre-Omicron variants. This suggests that a single infection may not generate the protective immunity required to defend against Omicron reinfections. Continued next-generation sequencing and inclusion of clinical metadata is necessary for effective surveillance, treatment, vaccine development, and public health recommendations.
COMMUNICATIONS BIOLOGY
(2023)
Article
Virology
Josep Quer, Sergi Colomer-Castell, Carolina Campos, Cristina Andres, Maria Pinana, Maria Francesca Cortese, Alejandra Gonzalez-Sanchez, Damir Garcia-Cehic, Marta Ibanez, Tomas Pumarola, Francisco Rodriguez-Frias, Andres Anton, David Tabernero
Summary: Virus pandemics are inevitable and have been accelerated by human activities. To effectively control and prevent pandemics, it is crucial to develop barriers based on knowledge rather than physical walls. Next-generation sequencing has proven to be a powerful tool in detecting and identifying infectious agents, developing vaccines and antiviral drugs, and understanding viral transmission dynamics and variants.
Article
Biology
Hendrick Gao-Min Lim, Shih-Hsin Hsiao, Yuan-Chii Gladys Lee
Summary: Coronavirus disease 2019 (COVID-19), following the swine flu in 2009, remains a challenge in accurately identifying a large number of samples. By integrating next-generation sequencing and cloud computing, this study developed an optimized workflow using a specific identification algorithm. Results show higher accuracy in distinguishing between the two pandemics, especially when using indices that represent each dataset exclusively.