Advanced Molecular Detection Clips Content (Published on 07/01/2021)
NEWS
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East Asia was hit by another coronavirus epidemic 20,000 years ago, new study shows
Sood A, Wang Z. CNN, Jun 25, 2021. -
A Lack of COVID-19 Genomes Could Prolong the Pandemic
Changoiwala P. Quanta, Jun 28 2021. -
Why Uruguay lost control of COVID
Taylor L. Nature, Jun 25, 2021. -
Wastewater-Based Epidemiology Booming With New Funding, CDC Program
Johnson M. GenomeWeb, Jun 23, 2021. -
CureVac, the latest experimental coronavirus vaccine, proves just 48 percent effective overall, a disappointing result
Johnson CY. Washington Post, Jun 30, 2021. -
Why most people who now die with Covid in England have had a vaccination
Spiegelhalter D, Masters A. Guardian, Jun 27, 2021. -
Building a pandemic-proof vaccine
O'Leary K. Nat Med, Jun 30, 2021. -
CRISPR-Based Wearable Diagnostics Enable SARS-CoV-2 Detection Through Mask
Rizk C. GenomeWeb, Jun 29, 2021. -
CDC probes how people contracted a dangerous infection found in the tropics--without leaving the U.S.
Shepherd K. Washington Post, Jul 1, 2021.
EVENTS / TRAINING / WEB RESOURCES
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SARS-CoV-2 variants of concern and variants under investigation in England
Public Health England, Technical Briefing 17, Jun 26, 2021. -
25 June 2021 Risk assessment for SARS-CoV-2 variant: Delta (VOC-21APR-02, B.1.617.2) Public Health England
Public Health England, Jun 25, 2021. -
SARS-CoV-2 variant data update, England
Public Health England, Version 7, Jun 25, 2021.
CONCEPTS / COMMENTS
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Contributions of the international plant science community to the fight against human infectious diseases - part 1: epidemic and pandemic diseases.
Lobato Gómez Maria et al. Plant biotechnology journal 2021 6 -
Beyond coronavirus: the virus discoveries transforming biology
Dance A. Nature, Jun 30, 2021.
METHODS / TOOLS
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Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review.
Singh Reema et al. Briefings in functional genomics 2021 6 -
Inferring environmental transmission using phylodynamics: a case-study using simulated evolution of an enteric pathogen.
Dawson Daniel et al. Journal of the Royal Society, Interface 2021 6 (179) 20210041 -
SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data.
Gabbassov Einar et al. Microbial genomics 2021 6 (6) -
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.
Nayfach Stephen et al. Nature microbiology 2021 6 (7) 960-970 -
Interactive SARS-CoV-2 mutation timemaps.
Warren René L et al. F1000Research 2021 6 68 -
Tracking SARS-CoV-2 Spike Protein Mutations in the United States (2020/01 - 2021/03) Using a Statistical Learning Strategy.
Zhao Lue Ping et al. bioRxiv : the preprint server for biology 2021 6
EVOLUTION / ECOLOGY / POPULATIONS
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Dynamics of the human nasal microbiota and Staphylococcus aureus CC398 carriage in pig truck drivers across one workweek.
Ingham Anna Cäcilia et al. Applied and environmental microbiology 2021 7 AEM0122521 -
Exoproteomic analysis of two MLST clade 2 strains of Clostridioides difficile from Latin America reveal close similarities.
de Melo Pacífico Dvison et al. Scientific reports 2021 6 (1) 13273 -
Microbiology of the American Smokeless Tobacco.
Rivera A J et al. Applied microbiology and biotechnology 2021 6 (12) 4843-4853 -
Salmonella Newport outbreak in Brazilian parrots: confiscated birds from the illegal pet trade as possible zoonotic sources.
Saidenberg André B S et al. Environmental microbiology reports 2021 6 -
Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains.
Seth-Smith Helena M B et al. Microbial genomics 2021 6 (6) -
The effect of recombination on the evolution of a population of Neisseria meningitidis.
MacAlasdair Neil et al. Genome research 2021 6 -
Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak
Bokalanga TW, et al. bioRxiv, Jun 29, 2021. -
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda.
Bugembe Daniel Lule et al. Nature microbiology 2021 6 -
Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil.
Slavov Svetoslav Nanev et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 6 104976 -
Evolution, heterogeneity and global dispersal of cosmopolitan genotype of Dengue virus type 2.
Yenamandra Surya Pavan et al. Scientific reports 2021 7 (1) 13496 -
Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates.
Naicker Serisha D et al. Emerging microbes & infections 2021 6 1-24 -
Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus.
Spadar Anton et al. Parasites & vectors 2021 6 (1) 332
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Patterns of Antibiotic Nonsusceptibility Among Invasive Group A Streptococcus Infections-United States, 2006-2017.
Katherine Fay et al. Clin Infect Dis 2021 6 (11) 1957-1964 -
Dissemination of Klebsiella pneumoniae ST147 NDM-1 in Poland, 2015-19.
Biedrzycka M et al. The Journal of antimicrobial chemotherapy 2021 6 -
Heterogeneous Streptomycin Resistance Level Among Mycobacterium tuberculosis Strains From the Same Transmission Cluster.
Rocha Deisy M G C et al. Frontiers in microbiology 2021 6 659545 -
Phylogenetic relationship and genomic characterization of Salmonella Typhimurium strains isolated from swine in Brazil.
Seribelli Amanda Aparecida et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 6 104977 -
Molecular epidemiology and drug-resistance of tuberculosis in Luodian revealed by whole genome sequencing.
Liu Mei et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 6 104979 -
Risk of hospitalisation associated with infection with SARS-CoV-2 lineage B.1.1.7 in Denmark: an observational cohort study.
Bager Peter et al. The Lancet. Infectious diseases 2021 6 -
Genome-wide association analysis of COVID-19 mortality risk in SARS-CoV-2 genomes identifies mutation in the SARS-CoV-2 spike protein that colocalizes with P.1 of the Brazilian strain.
Hahn Georg et al. Genetic epidemiology 2021 6 -
Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Gobeil Sophie M-C et al. Science (New York, N.Y.) 2021 6 -
Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants.
Cai Yongfei et al. Science (New York, N.Y.) 2021 6 -
Transmitted Drug Resistance Among HIV-1 Diagnoses in the United States, 2014-2018.
McClung R Paul et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 6 -
The Molecular Epidemiology and Clinical Phylogenetics of Rhinoviruses among Paediatric Cases in Sydney, Australia.
Adam Dillon Charles et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 6
DETECTION / DIAGNOSIS
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Molecular characterization and improved diagnostics of Nocardia strains isolated over the last two decades at a German tertiary care center.
Chhatwal Patrick et al. EXCLI journal 2021 6 851-862 -
Loop-mediated isothermal amplification (LAMP) assay targeting RLEP for detection of Mycobacterium leprae in leprosy patients.
Jiang Haiqin et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 4 145-152 -
Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance
Maidana-Kulesza MN, et al. medRxiv, Jun 29, 2021. -
Surveillance for SARS-CoV-2 variants of concern in the Australian context.
Andersson Patiyan et al. The Medical journal of Australia 2021 6 (11) 500-502.e1 -
A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance.
Bourassa Lori et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2021 6 104900 -
Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State.
Perchetti Garrett A et al. Journal of medical virology 2021 6 -
Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner
Gregory DA, et al. medRxiv, Jun 26, 2021. -
LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding.
Ludwig Kerstin U et al. Nature biotechnology 2021 7 -
Detection of SARs-CoV-2 in wastewater using the existing environmental surveillance network: A potential supplementary system for monitoring COVID-19 transmission.
Sharif Salmaan et al. PloS one 2021 6 (6) e0249568 -
Rapid screening method for the detection of SARS-CoV-2 variants of concern: Rapid screening of SARS-CoV-2 variants of concern.
Ong David S Y et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2021 6 104903 -
Prevalence of hepatitis delta virus among chronic hepatitis B carriers in a large tertiary center in the Netherlands.
Beudeker Boris J B et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2021 6 104870 -
Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados.
Thannesberger J et al. Parasites & vectors 2021 7 (1) 343 -
Detection of Crimean-Congo hemorrhagic fever virus in blood-fed Hyalomma ticks collected from Mauritanian livestock.
Schulz A et al. Parasites & vectors 2021 7 (1) 342 -
Invasive aspergillosis due to Aspergillus cryptic species: a prospective multicenter study.
Imbert Sebastien et al. Mycoses 2021 6 -
Preventing Chagas disease: A new RT-qPCR method for rapid and specific quantification of viable Trypanosoma cruzi for food safety.
de Oliveira Ana Caroline et al. Food research international (Ottawa, Ont.) 2021 6 110368 -
Multiplex PCR assay for the identification of eight Anopheles species belonging to the Hyrcanus, Barbirostris and Lindesayi groups.
Bang Woo Jun et al. Malaria journal 2021 6 (1) 287
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Mycobacterium chimaera Genomics With Regard to Epidemiological and Clinical Investigations Conducted for an Open Chest Postsurgical Mycobacterium chimaera Infection Outbreak.
Lecorche Emmanuel et al. Open forum infectious diseases 2021 7 (6) ofab192 -
A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains.
Miles-Jay Arianna et al. Microbial genomics 2021 6 (6) -
Assessing a transmission network of Mycobacterium tuberculosis in an African city using single nucleotide polymorphism threshold analysis.
Yassine Edriss et al. MicrobiologyOpen 2021 6 (3) e1211 -
Whole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019.
Joensen Katrine Grimstrup et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 6 (22) -
Metagenomic next-generation sequencing in the family outbreak of psittacosis: First reported family outbreak of psittacosis in China under COVID-19.
Li Na et al. Emerging microbes & infections 2021 6 1-31 -
COVID-19 Transmission among Healthcare Workers at a Quarantine Facility in Thailand: Genomic and Outbreak Investigations.
Atsawawaranunt Kamolthip et al. The American journal of tropical medicine and hygiene 2021 6 -
Molecular Epidemiology of SARS-CoV-2 in Greece Reveals Low Rates of Onward Virus Transmission after Lifting of Travel Restrictions Based on Risk Assessment during Summer 2020.
Kostaki Evangelia Georgia et al. mSphere 2021 7 e0018021 -
SARS-CoV-2 under an elimination strategy in Hong Kong.
Gu Haogao et al. medRxiv : the preprint server for health sciences 2021 7 -
Resurgence of SARS-CoV-2 in India: Potential role of the B.1.617.2 (Delta) variant and delayed interventions
Salvatore M, et al. medRxiv, Jun 30, 2021. -
Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface.
Li Kathy K et al. The Journal of infection 2021 4 (1) 96-103 -
Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru.
Juscamayta-López Eduardo et al. Journal of medical virology 2021 6 -
Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management.
Page Andrew J et al. Microbial genomics 2021 6 (6) -
Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.
Stirrup Oliver et al. eLife 2021 6 -
Characterization of SARS-CoV-2 infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker Andreas et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 6 -
Phylogenetic analysis in the clinical risk management of an outbreak of Hepatitis C Virus infection among transfused thalassemia patients in Italy.
Mazzucco Walter et al. The Journal of hospital infection 2021 6 -
St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event.
Ridenour Chase L et al. Frontiers in genetics 2021 6 667895
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State.
McEwen Abbye E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 6 -
Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: A pilot randomised placebo-controlled trial.
Wilson Brooke C et al. EBioMedicine 2021 6 103443 -
Prevention and Attenuation of Covid-19 with the BNT162b2 and mRNA-1273 Vaccines.
Thompson Mark G et al. The New England journal of medicine 2021 7 -
Myocarditis Occurring After Immunization With mRNA-Based COVID-19 Vaccines.
Shay David K et al. JAMA cardiology 2021 6 -
Patients With Acute Myocarditis Following mRNA COVID-19 Vaccination.
Kim Han W et al. JAMA cardiology 2021 6 -
Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine.
Heath Paul T et al. The New England journal of medicine 2021 7
HOST-MICROBE INTERACTIONS
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Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation.
Ingham Anna Cäcilia et al. Microbiome 2021 6 (1) 148 -
Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity.
Raffelsberger Niclas et al. Gut microbes 2021 6 (1) 1939599 -
The landscape of antibody binding in SARS-CoV-2 infection.
Heffron Anna S et al. PLoS biology 2021 6 (6) e3001265 -
Influence of APOE locus on poor prognosis of COVID-19.
Rodriguez JCG, et al. Heliyon, Jun 23, 2021. -
SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern
MacCallum M, et al. Science, Jul 1, 2021. -
Associations of IL13 gene polymorphisms and immune factors with Schistosoma haematobium infection in schoolchildren in four schistosomiasis-endemic communities in Ghana.
Sarpong-Baidoo Margaret et al. PLoS neglected tropical diseases 2021 6 (6) e0009455
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Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by Public Health Genomics Branch to provide current awareness of the scientific literature and news. Inclusion in the clips does not necessarily represent the views of the Centers for Disease Control and Prevention nor does it imply endorsement of the article's methods or findings. CDC and DHHS assume no responsibility for the factual accuracy of the items presented. The selection, omission, or content of items does not imply any endorsement or other position taken by CDC or DHHS. Opinion, findings and conclusions expressed by the original authors of items included in the Clips, or persons quoted therein, are strictly their own and are in no way meant to represent the opinion or views of CDC or DHHS. References to publications, news sources, and non-CDC Websites are provided solely for informational purposes and do not imply endorsement by CDC or DHHS.
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- Page last updated:Sep 5, 2024