A laboratory framework for ongoing optimization of amplification-based genomic surveillance programs

Autor: Connie Lam, Jessica Johnson-Mackinnon, Kerri Basile, Winkie Fong, Carl J.E. Suster, Mailie Gall, Jessica Agius, Shona Chandra, Jenny Draper, Elena Martinez, Alexander Drew, Qinning Wang, Sharon C. Chen, Jen Kok, Dominic E. Dwyer, Vitali Sintchenko, Rebecca J. Rockett

Publikováno v: Microbiology Spectrum, Vol 11, Iss 6 (2023)

ABSTRACT Constantly evolving viral populations affect the specificity of primers and the quality of genomic surveillance. This study presents a framework for the continuous optimization of sequencing efficiency for public health surveillance based on

Externí odkaz: https://doaj.org/article/c8506cf497274da69108601f2e1d8cca

Emergent Omicron BR.2.1 sublineage of SARS-CoV-2 in New South Wales, Australia: a subvariant with high fitness but without increased disease severity

Autor: Annaleise R Howard-Jones, Alicia Arnott, Jenny Draper, Mailie Gall, Sally Ellis, Kelsi Marris, Christine Selvey, Kerri Basile, Dominic E Dwyer, Vitali Sintchenko, Jen Kok

Publikováno v: International Journal of Infectious Diseases, Vol 130, Iss , Pp 38-41 (2023)

Objectives: To describe the epidemiology and impact of Omicron BR.2.1, an emergent SARS-CoV-2 Omicron BA.2.75 sublineage displaying high fitness compared to other cocirculating subvariants in New South Wales, Australia. Methods: From September 01 to

Externí odkaz: https://doaj.org/article/95dcd0cf691e471799c6ca2e4236ca4e

Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis

Autor: Lijuan Luo, Michael Payne, Qinning Wang, Sandeep Kaur, Irani U. Rathnayake, Rikki Graham, Mailie Gall, Jenny Draper, Elena Martinez, Sophie Octavia, Mark M. Tanaka, Amy V. Jennison, Vitali Sintchenko, Ruiting Lan

Publikováno v: Microbiology Spectrum, Vol 11, Iss 1 (2023)

ABSTRACT Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. In this study, a total of 568 S. Enteritidis isolates from two Australian states across two consecutive years were analyzed and compared to i

Externí odkaz: https://doaj.org/article/ec0fed3056bf4d468c1291f60a25a86e

Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection

Autor: Carl J. E. Suster, Alicia Arnott, Grace Blackwell, Mailie Gall, Jenny Draper, Elena Martinez, Alexander P. Drew, Rebecca J. Rockett, Sharon C.-A. Chen, Jen Kok, Dominic E. Dwyer, Vitali Sintchenko

Publikováno v: Frontiers in Public Health, Vol 10 (2022)

Genomic surveillance of SARS-CoV-2 has been essential to inform public health response to outbreaks. The high incidence of infection has resulted in a smaller proportion of cases undergoing whole genome sequencing due to finite resources. We present

Externí odkaz: https://doaj.org/article/d01f1ef409bf462c8dbaf704c2cd6af4

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review: 3 approved]

Autor: Áine O'Toole, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad Hassan, Tamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Swiss Viollier Sequencing Consortium, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-Nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), Tulio de Oliveira, Nuno Faria, Andrew Rambaut, Moritz U. G. Kraemer

Publikováno v: Wellcome Open Research, Vol 6 (2021)

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from ro

Externí odkaz: https://doaj.org/article/63672d265a40472ea7302adbef66d81f