Advanced Molecular Detection Clips Content (Published on 09/30/2021)
NEWS
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Accelerated Growth of Decentralized Testing Expected to Continue Beyond COVID-19
O'Connor L. 360dx, Sep 22, 2021. -
Trevor Bedford: Two Astounding Awards For Virologist Who Raised Early COVID Alarms
NPR, Sep 28, 2021. -
Closest known relatives of virus behind COVID-19 found in Laos
Mallapaty S. Nature, Sep 24, 2021. -
Resistance to front-line malaria drugs confirmed in Africa
Kozlov M. Nature, Sep 23, 2021.
CONCEPTS / COMMENTS
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The future of zoonotic risk prediction.
Carlson Colin J et al. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2021 9 (1837) 20200358 -
Genomic signatures for predicting the zoonotic potential of novel viruses.
Ladner Jason T et al. PLoS biology 2021 9 (9) e3001403 -
Coordinating SARS-CoV-2 genomic surveillance in the United States.
Nelson Martha I et al. Virus evolution 2021 9 (2) veab053 -
Clinical evidence that the pandemic from 1889 to 1891 commonly called the Russian flu might have been an earlier coronavirus pandemic.
Brüssow Harald et al. Microbial biotechnology 2021 7 (5) 1860-1870 -
Flies, cockroaches and AMR
(editorial) Nat Microbiol, Sep 27, 2021.
METHODS / TOOLS
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Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.
Labbé Geneviève et al. Microbial genomics 2021 9 (9) -
Comparison of four enzymatic library preparation kits for sequencing Shiga toxin-producing Escherichia coli for surveillance and outbreak detection.
Truong Jenny et al. Journal of microbiological methods 2021 9 106329
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Protocol for safe, affordable, and reproducible isolation and quantitation of SARS-CoV-2 RNA from wastewater.
Trujillo Monica et al. PloS one 2021 9 (9) e0257454 -
Multiple Occurrences of a 168-Nucleotide Deletion in SARS-CoV-2 ORF8, Unnoticed by Standard Amplicon Sequencing and Variant Calling Pipelines.
Brandt David et al. Viruses 2021 9 (9)
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An ultrafast SARS-CoV-2 virus enrichment and extraction method compatible with multiple modalities for RNA detection.
Dignan Leah M et al. Analytica chimica acta 2021 9 338846
EVOLUTION / ECOLOGY / POPULATIONS
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Different evolutionary trends form the twilight zone of the bacterial pan-genome.
Horesh Gal et al. Microbial genomics 2021 9 (9) -
Tracking Fecal Bacterial Dispersion from Municipal Wastewater to Peri-Urban Farms during Monsoon Rains in Hue City, Vietnam.
Prayoga Windra et al. International journal of environmental research and public health 2021 9 (18)
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Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina.
Gagetti Paula et al. Microbial genomics 2021 9 (9)
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Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages.
Calland Jessica K et al. PLoS genetics 2021 9 (9) e1009829 -
Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates.
Schrörs Barbara et al. PloS one 2021 9 (9) e0249254 -
Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh.
Ahammad Ishtiaque et al. PloS one 2021 9 (9) e0258019 -
Emergence and phenotypic characterization of C.1.2, a globally detected lineage that rapidly accumulated mutations of concern
Scheepers C, et al. medRxiv, Sep 24, 2021. -
Estimating the strength of selection for new SARS-CoV-2 variants
van Dorp CH, et al. medRxiv, Sep 24, 2021. -
Genomic Surveillance in Japan of AY.29 --A New Sub-lineage of SARS-CoV-2 Delta Variant with C5239T and T5514C Mutations
Abe T, et al. medRxiv, Sep 23, 2021. -
SARS-CoV-2 B.1.1.7 lineage rapidly spreads and replaces R.1 lineage in Japan: Serial and stationary observation in a community.
Hirotsu Yosuke et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 9 105088 -
Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America.
Jian Ming-Jr et al. PeerJ 2021 9 e11991 -
Origin, phylogeny, variability and epitope conservation of SARS-CoV-2 worldwide.
Vale Filipa F et al. Virus research 2021 8 198526 -
Genomic Analysis Illustrated a Single Introduction and Evolution of Israeli Bluetongue Serotype 8 Virus Population 2008-2019.
Golender Natalia et al. Microorganisms 2021 9 (9) -
Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children.
Han Alvin X et al. eLife 2021 8
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Consistency of spatial dynamics of HIV-1 and HCV among HIV-1/HCV coinfected drug users in China.
Wang Yu et al. BMC infectious diseases 2021 9 (1) 1001 -
Genetic and Antigenic Characterization of an Influenza A(H3N2) Outbreak in Cambodia and the Greater Mekong Subregion during the COVID-19 Pandemic, 2020.
Siegers Jurre Y et al. Journal of virology 2021 9 JVI0126721
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Population genetic structure of the malaria vector Anopheles minimus in Thailand based on mitochondrial DNA markers.
Bunmee Kamonchanok et al. Parasites & vectors 2021 9 (1) 496
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genomic and phenotypic comparison of two Salmonella Typhimurium strains responsible for consecutive salmonellosis outbreaks in New Zealand.
Bloomfield Samuel J et al. International journal of medical microbiology : IJMM 2021 9 (7) 151534 -
Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste.
Jarocki Veronica M et al. Frontiers in microbiology 2021 9 731050 -
Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis.
Kalizang'oma Akuzike et al. Microbial genomics 2021 9 (9)
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Recent advances in understanding and combatting Neisseria gonorrhoeae: a genomic perspective.
Harrison Odile B et al. Faculty reviews 2021 9 65 -
A one health genomic investigation of gentamicin resistance in Salmonella from human and chicken sources in Canada, 2014-2017.
Cox Graham W et al. Antimicrobial agents and chemotherapy 2021 9 AAC0096621 -
Identifying and prioritizing potential human-infecting viruses from their genome sequences.
Mollentze Nardus et al. PLoS biology 2021 9 (9) e3001390 -
Prevalence of Resistance-Associated Substitutions and Phylogenetic Analysis of Hepatitis C Virus Infection in Russia.
Isakov Vasily et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 9 -
A whole transcriptomic approach provides novel insights into the molecular basis of organophosphate and pyrethroid resistance in Anopheles arabiensis from Ethiopia.
Messenger Louisa A et al. Insect biochemistry and molecular biology 2021 9 103655
DETECTION / DIAGNOSIS
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In silico species identification and serotyping for Cronobacter isolates by use of whole-genome sequencing data.
Wang Lu et al. International journal of food microbiology 2021 9 109405 -
Resistance profiles and diversity of β-lactamases in Escherichia coli strains isolated from city-scale sewage surveillance in Bergen, Norway mimic clinical prevalence.
Grevskott Didrik H et al. Ecotoxicology and environmental safety 2021 9 112788 -
A High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA.
Bourdin Thibault et al. Applied and environmental microbiology 2021 9 AEM0139921 -
Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents.
Jahan Nusrat A et al. Pathogens (Basel, Switzerland) 2021 9 (9) -
Exploring the value of MALDI-TOF MS for the detection of clonal outbreaks of Burkholderia contaminans.
Fiamanya Selali et al. Journal of microbiological methods 2021 1 106130 -
Use of real-time PCR as an alternative to conventional genotyping methods for the laboratory detection of lymphogranuloma venereum (LGV).
Woodson Evonne N et al. Diagnostic microbiology and infectious disease 2021 9 (4) 115532
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Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding.
Wilkinson David A et al. PloS one 2021 9 (9) e0257971 -
Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system
Bohl JA, et al. medRxiv, Sep 28, 2021. -
Analytical performance comparison of four SARS-CoV-2 RT-qPCR primer-probe sets for wastewater samples.
Zhang Shuxin et al. The Science of the total environment 2021 9 150572 -
Serological Testing Reveals the Hidden COVID-19 Burden among Health Care Workers Experiencing a SARS-CoV-2 Nosocomial Outbreak.
Nakagama Yu et al. Microbiology spectrum 2021 9 e0108221
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RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants.
Rothman Jason A et al. Applied and environmental microbiology 2021 9 AEM0144821 -
Assessment of a Program for SARS-CoV-2 Screening and Environmental Monitoring in an Urban Public School District.
Crowe John et al. JAMA network open 2021 9 (9) e2126447
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Tracking the temporal variation of COVID-19 surges through wastewater-based epidemiology during the peak of the pandemic: a six-month long study in Charlotte, North Carolina
Barua VB, et al. medRxiv, Sep 24, 2021. -
Effectiveness and cost-effectiveness of four different strategies for SARS-CoV-2 surveillance in the general population (CoV-Surv Study): study protocol for a two-factorial randomized controlled multi-arm trial with cluster sampling.
Deckert Andreas et al. Trials 2021 9 (1) 656 -
A targeted approach with nanopore sequencing for the universal detection and identification of flaviviruses.
Reteng Patrick et al. Scientific reports 2021 9 (1) 19031 -
Urinary genome detection and tracking of Hantaan virus from hemorrhagic fever with renal syndrome patients using multiplex PCR-based next-generation sequencing.
Cho Seungchan et al. PLoS neglected tropical diseases 2021 9 (9) e0009707 -
Development of nucleic-acid lateral flow immunoassay for rapid and accurate detection of Chikungunya virus in Indonesia.
Ajie Mandala et al. Journal of microbiology and biotechnology 2021 9 (12)
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European Non-Polio Enterovirus Network: Introduction of Hospital-Based Surveillance Network to Understand the True Disease Burden of Non-Polio Enterovirus and Parechovirus Infections in Europe
Harvala H, et al. Microorganisms. 2021 Aug 27;9(9):1827. -
Diagnostic Allele-Specific PCR for the Identification of Candida auris Clades.
Carolus Hans et al. Journal of fungi (Basel, Switzerland) 2021 9 (9) -
Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia.
Feleke Sindew M et al. Nature microbiology 2021 9 (10) 1289-1299
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A gene expression panel for estimating age in males and females of the sleeping sickness vector Glossina morsitans.
Lucas Eric R et al. PLoS neglected tropical diseases 2021 9 (9) e0009797
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India.
Sharma Shashi et al. Scientific reports 2021 9 (1) 18126 -
Interventions to Disrupt Coronavirus Disease Transmission at a University, Wisconsin, USA, August-October 2020.
Currie Dustin W et al. Emerging infectious diseases 2021 9 (11)
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Emergence of an early SARS-CoV-2 epidemic in the United States.
Zeller Mark et al. Cell 2021 9 (19) 4939-4952.e15 -
The impact of real-time whole genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks.
Francis Rodric V et al. The Journal of infectious diseases 2021 9
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Management following the first confirmed case of SARS-CoV-2 in a domestic cat associated with a massive outbreak in South Korea.
Han Taewon et al. One health (Amsterdam, Netherlands) 2021 9 100328 -
Incorporating metadata in HIV transmission network reconstruction: A machine learning feasibility assessment.
Mazrouee Sepideh et al. PLoS computational biology 2021 9 (9) e1009336 -
Re-Emergence and Spread of Haemorrhagic Septicaemia in Germany: The Wolf as a Vector?
Kutzer Peter et al. Microorganisms 2021 9 (9)
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Precise quantification of bacterial strains after fecal microbiota transplantation delineates long-term engraftment and explains outcomes
Aggarwala V, et al. Nat Microbiol, Sep 27, 2021.
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Effectiveness of BNT162b2 Vaccine in Adolescents during Outbreak of SARS-CoV-2 Delta Variant Infection, Israel, 2021.
Glatman-Freedman Aharona et al. Emerging infectious diseases 2021 9 (11) -
COVID-19 Vaccine Breakthrough Infections in the Veterans Health Administration.
Sharma A, et al. medRxiv, Sep 26, 2021. -
Sustained Replication of Synthetic Canine Distemper Virus Defective Genomes In Vitro and In Vivo.
Tilston-Lunel Natasha L et al. mSphere 2021 9 e0053721
HOST-MICROBE INTERACTIONS
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Host genetics of pediatric SARS-CoV-2 COVID-19 and multisystem inflammatory syndrome in children.
Schulert Grant S et al. Current opinion in pediatrics 2021 9 -
A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance.
Anisul Mohd et al. eLife 2021 8 -
Defining variant-resistant epitopes targeted by SARS-CoV-2 antibodies: A global consortium study.
Hastie Kathryn M et al. Science (New York, N.Y.) 2021 9 eabh2315 -
A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences.
James Stephen Among et al. BMC genomics 2021 9 (Suppl 3) 700
indicates that at least one CDC-affiliated author; indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice. 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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