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1.
Frontiers in public health ; 10, 2022.
Article in English | EuropePMC | ID: covidwho-2073841

ABSTRACT

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 a framework for estimating the impact of reduced depths of genomic surveillance on the resolution of outbreaks, based on a clustering approach using pairwise genetic and temporal distances. We apply the framework to simulated outbreak data to show that outbreaks are detected less frequently when fewer cases are subjected to whole genome sequencing. The impact of sequencing fewer cases depends on the size of the outbreaks, and on the genetic and temporal similarity of the index cases of the outbreaks. We also apply the framework to an outbreak of the SARS-CoV-2 Delta variant in New South Wales, Australia. We find that the detection of clusters in the outbreak would have been delayed if fewer cases had been sequenced. Existing recommendations for genomic surveillance estimate the minimum number of cases to sequence in order to detect and monitor new virus variants, assuming representative sampling of cases. Our method instead measures the resolution of clustering, which is important for genomic epidemiology, and accommodates sampling biases.

2.
Nat Commun ; 13(1): 2745, 2022 05 18.
Article in English | MEDLINE | ID: covidwho-1931393

ABSTRACT

Co-infections with different variants of SARS-CoV-2 are a key precursor to recombination events that are likely to drive SARS-CoV-2 evolution. Rapid identification of such co-infections is required to determine their frequency in the community, particularly in populations at-risk of severe COVID-19, which have already been identified as incubators for punctuated evolutionary events. However, limited data and tools are currently available to detect and characterise the SARS-CoV-2 co-infections associated with recognised variants of concern. Here we describe co-infection with the SARS-CoV-2 variants of concern Omicron and Delta in two epidemiologically unrelated adult patients with chronic kidney disease requiring maintenance haemodialysis. Both variants were co-circulating in the community at the time of detection. Genomic surveillance based on amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified subpopulations of Delta and Omicron viruses in respiratory samples. These findings highlight the importance of integrated genomic surveillance in vulnerable populations and provide diagnostic pathways to recognise SARS-CoV-2 co-infection using genomic data.


Subject(s)
COVID-19 , Coinfection , Genomics , Humans , SARS-CoV-2/genetics
3.
Transplantation ; 106(9): 1860-1866, 2022 09 01.
Article in English | MEDLINE | ID: covidwho-1891227

ABSTRACT

BACKGROUND: Since November 2021, a new variant of concern (VOC), the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.1.529 (Omicron) has emerged as the dominant coronavirus disease 2019 (COVID-19) infection worldwide. We describe the clinical presentation, risk factors, and outcomes in a cohort of kidney and kidney pancreas transplant recipients with COVID-19 caused by Omicron infection. METHODS: We included all kidney and kidney pancreas transplant recipients diagnosed with SARS-CoV-2 Omicron infections between December 26, 2021, and January 14, 2022, in a single transplant center in Australia. Identification of the VOC Omicron was confirmed using phylogenetic analysis of SARS-CoV-2 sequences. RESULTS: Forty-one patients with kidney (6 living and 33 deceased) and kidney pancreas transplants were diagnosed with the VOC Omicron (lineage B.1.1.529/BA.1) infection during the study period. The mean age (SD) at the time of diagnosis was 52 (11.1) y; 40 (out of 41) (98%) had received at least 2 doses of COVID-19 vaccine. Cough was the most frequent symptom (80.5%), followed by myalgia (70.7%), sore throat (63.4%), and fever (58.5%). After a follow-up time of 30 d, 1 (2.4%) patient died, 2 (4.9%) experienced multiorgan failure, and 5 (12.2%) had respiratory failure; 11 (26.8%) patients developed other superimposed infections. Compared with recipients who did not receive sotrovimab antibody therapy, the odds ratio (95% confidence interval) for hospitalization among patients who received sotrovimab was 0.05 (0.005-0.4). CONCLUSIONS: Despite double or triple dose vaccination, VOC Omicron infections in kidney and kidney pancreas transplant recipients are not necessarily mild. Hospitalization rates remained high (around 56%), and sotrovimab use may prevent hospitalization.


Subject(s)
COVID-19 Vaccines , COVID-19 , SARS-CoV-2 , Antibodies, Monoclonal, Humanized , Antibodies, Neutralizing , COVID-19 Vaccines/adverse effects , Humans , Kidney , Pancreas , Phylogeny , Risk Factors , Transplant Recipients
4.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-337287

ABSTRACT

The emergence of resistance to antiviral drugs increasingly used to treat SARS-CoV-2 infections has been recognised as a significant threat to COVID-19 control. In addition, some SARS-CoV-2 variants of concern appear to be intrinsically resistant to several classes of these antiviral agents. Therefore, there is a critical need for rapid recognition of clinically relevant polymorphisms in SARS-CoV-2 genomes associated with significant reduction of drug activity in virus neutralisation experiments. Here we present SABRes, a bioinformatic tool, which leverages on expanding public datasets of SARS-CoV-2 genomes and allows detection of drug resistance mutations in consensus genomes as well as in viral subpopulations. We have applied SABRes to detect resistance-conferring mutations in over 25,000 genomes generated over the course of the SARS-CoV-2 pandemic in Australia.

6.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327656

ABSTRACT

We identified the co-infection of the SARS-CoV-2 Omicron and Delta variants in two epidemiologically unrelated patients with chronic kidney disease requiring haemodialysis. Both SARS-CoV-2 variants were co-circulating locally at the time of detection. Amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified Omicron and Delta subpopulations in respiratory samples from the two patients. These findings highlight the importance of genomic surveillance in vulnerable populations.

7.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-305797

ABSTRACT

Objective: To adapt ‘fishplots’ to describe SARS-CoV-2 genomic cluster evolution. Results: : This novel analysis adapted the fishplot to depict the size and duration of circulating genomic clusters over time in New South Wales, Australia. It illuminated the effectiveness of interventions on the emergence, spread and eventual elimination of clusters and distilled genomic data into clear information to inform public health action.

8.
O'Toole, Áine, Hill, Verity, Pybus, Oliver, Watts, Alexander, Bogoch, Issac, Khan, Kamran, Messina, Jane, Tegally, Houriiyah, Lessells, Richard, Giandhari, Jennifer, Pillay, Sureshnee, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo, Mine, Madisa, Tokajian, Sima, Hassan, Hamad, Salloum, Tamara, Merhi, Georgi, Koweyes, Jad, Geoghegan, Jemma, de Ligt, Joep, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki, Pattabiraman, Chitra, Prasad, Pramada, Desai, Anita, Vasanthapuram, Ravi, Schulz, Thomas, Steinbrück, Lars, Stadler, Tanja, Parisi, Antonio, Bianco, Angelica, García de Viedma, Darío, Buenestado-Serrano, Sergio, Borges, Vítor, Isidro, Joana, Duarte, Sílvia, Gomes, João Paulo, Zuckerman, Neta, Mandelboim, Michal, Mor, Orna, Seemann, Torsten, Arnott, Alicia, Draper, Jenny, Gall, Mailie, Rawlinson, William, Deveson, Ira, Schlebusch, Sanmarié, McMahon, Jamie, Leong, Lex, Lim, Chuan Kok, Chironna, Maria, Loconsole, Daniela, Bal, Antonin, Josset, Laurence, Holmes, Edward, St. George, Kirsten, Lasek-Nesselquist, Erica, Sikkema, Reina, Oude Munnink, Bas, Koopmans, Marion, Brytting, Mia, Sudha rani, V.; Pavani, S.; Smura, Teemu, Heim, Albert, Kurkela, Satu, Umair, Massab, Salman, Muhammad, Bartolini, Barbara, Rueca, Martina, Drosten, Christian, Wolff, Thorsten, Silander, Olin, Eggink, Dirk, Reusken, Chantal, Vennema, Harry, Park, Aekyung, Carrington, Christine, Sahadeo, Nikita, Carr, Michael, Gonzalez, Gabo, de Oliveira, Tulio, Faria, Nuno, Rambaut, Andrew, Kraemer, Moritz, The, Covid-Genomics U. K. consortium, Network for Genomic Surveillance in South, Africa, Brazil, U. K. Cadde Genomic Network, Swiss Viollier Sequencing, Consortium, Diego, Search Alliance San, National Virus Reference, Laboratory, Seq, Covid Spain, Danish Covid-19 Genome, Consortium, Communicable Diseases Genomic, Network, Dutch National, Sars-CoV-surveillance program, Division of Emerging Infectious, Diseases.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-318194

ABSTRACT

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 routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

9.
BMC Res Notes ; 14(1): 415, 2021 Nov 17.
Article in English | MEDLINE | ID: covidwho-1523326

ABSTRACT

OBJECTIVE: To adapt 'fishplots' to describe real-time evolution of SARS-CoV-2 genomic clusters. RESULTS: This novel analysis adapted the fishplot to depict the size and duration of circulating genomic clusters over time in New South Wales, Australia. It illuminated the effectiveness of interventions on the emergence, spread and eventual elimination of clusters and distilled genomic data into clear information to inform public health action.


Subject(s)
COVID-19 , Australia , Genomics , Humans , New South Wales , SARS-CoV-2
10.
Public Health Res Pract ; 31(3)2021 Sep 08.
Article in English | MEDLINE | ID: covidwho-1399672

ABSTRACT

OBJECTIVES: To describe local operational aspects of the coronavirus disease 2019 (COVID-19) response during the first three waves of outbreaks in New South Wales (NSW), Australia, which began in January, July and December 2020. Type of program or service: Public health outbreak response. METHODS: Narrative with epidemiological linking and genomic testing. RESULTS: Epidemiological linking and genomic testing found that during the first wave of COVID-19 in NSW, a large number of community transmissions went undetected because of limited testing for the virus and limited contact tracing of cases. The second wave of COVID-19 in NSW emerged following reintroduction from the second wave in Victoria, Australia in July 2020, and the third wave followed undetected introduction from overseas. By the second and third waves, cases could be more effectively detected and isolated through an increased ability to test and contact trace, and to rapidly genomic sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolates, allowing most cases to be identified and epidemiologically linked. This greater certainty in understanding chains of transmission resulted in control of the outbreaks despite less stringent restrictions on the community, by using a refined strategy of targeted shutdown, restrictions on cases, their close contacts, identified hotspots and venues of concern rather than a whole of community lockdown. Risk assessments of potential transmission sites were constantly updated through our evolving experience with transmission events. However, this refined strategy did leave the potential for large point source outbreaks should any cases go undetected. [Addendum] A fourth wave that began in Sydney in June 2021 challenged this strategy due to the more transmissible nature of the Delta variant of SARS-CoV-2. LESSONS LEARNT: A wave of COVID-19 infections can develop quickly from one infected person. The community needs to remain vigilant, adhering to physical distancing measures, signing in to venues they visit, and getting tested if they have any symptoms. Signing out of venues on exit allows public health resources to be used more efficiently to respond to outbreaks.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Communicable Disease Control/methods , Disease Outbreaks/statistics & numerical data , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19 Testing/methods , Child , Child, Preschool , Communicable Disease Control/organization & administration , Contact Tracing/methods , Disease Outbreaks/prevention & control , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , New South Wales/epidemiology , Physical Distancing , Public Health , Quarantine/methods , SARS-CoV-2/isolation & purification , Victoria/epidemiology , Young Adult
11.
Wellcome Open Res ; 6: 121, 2021.
Article in English | MEDLINE | ID: covidwho-1259748

ABSTRACT

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 routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

12.
BMJ Case Rep ; 14(1)2021 Jan 18.
Article in English | MEDLINE | ID: covidwho-1066836

ABSTRACT

This case represents a rare fulminant course of fried-rice associated food poisoning in an immunocompetent person due to pre-formed exotoxin produced by Bacillus cereus, with severe manifestations of sepsis, including multi-organ (hepatic, renal, cardiac, respiratory and neurological) failure, shock, metabolic acidosis, rhabdomyolysis and coagulopathy. Despite maximal supportive measures (continuous renal replacement therapy, plasmapheresis, N-acetylcysteine infusion and blood products, and broad-spectrum antimicrobials) and input from a multidisciplinary team (consisting of infectious diseases, intensive care, gastroenterology, surgery, toxicology, immunology and haematology), mortality resulted. This case is the first to use whole genome sequencing techniques to confirm the toxigenic potential of B. cereus It has important implications for food preparation and storage, particularly given its occurrence in home isolation during the COVID-19 pandemic.


Subject(s)
Bacillus cereus/genetics , Exotoxins/genetics , Foodborne Diseases/diagnosis , Acetylcysteine/therapeutic use , Acidosis/physiopathology , Acidosis/therapy , Adult , Anti-Arrhythmia Agents/therapeutic use , Anti-Bacterial Agents/therapeutic use , Arrhythmias, Cardiac/physiopathology , Arrhythmias, Cardiac/therapy , Bacillus cereus/isolation & purification , Blood Coagulation Disorders/physiopathology , Blood Coagulation Disorders/therapy , Blood Transfusion , Brain Diseases , Continuous Renal Replacement Therapy , Fatal Outcome , Female , Foodborne Diseases/microbiology , Foodborne Diseases/physiopathology , Foodborne Diseases/therapy , Free Radical Scavengers/therapeutic use , Humans , Immunocompetence , Liver Failure/physiopathology , Liver Failure/therapy , Multiple Organ Failure/physiopathology , Multiple Organ Failure/therapy , Plasmapheresis , Renal Insufficiency/physiopathology , Renal Insufficiency/therapy , Rhabdomyolysis/physiopathology , Rhabdomyolysis/therapy , Sepsis/physiopathology , Sepsis/therapy , Shock/physiopathology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Whole Genome Sequencing
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