Advanced Molecular Detection Clips Content (Published on 11/18/2021)
NEWS
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New coronavirus, likely from dogs, infects people in Malaysia and Haiti
Doucleff M. NPR, Nov 5, 2021. -
Why is Delta so infectious? New lab tool spotlights little noticed mutation that speeds viral spread
Wadman M. Science, Nov 4, 2021. -
Prominent scientist who said lab-leak theory of covid-19 origin should be probed now believes evidence points to Wuhan market
Achenbach J. Washington Post, Nov 18, 2021. -
Brown University Researchers Develop RNA-Based Breath Test for COVID-19
Ketchum K. GenomeWeb, Nov 9, 2021. -
A prominent virologist warns COVID-19 pill could unleash dangerous mutants. Others see little cause for alarm
Service RF. Science, Nov 7, 2021. -
COVID antiviral pills: what scientists still want to know
Ledford H. Nature, Nov 10, 2021. -
Moderna and U.S. at Odds Over Vaccine Patent Rights
Stolberg SG and Robbins R. New York Times, Nov 11, 2021. -
Gene linked to doubling risk of COVID-19 death found by UK scientists
Aripaka P. Reuters, Nov 5, 2021. -
How do people resist COVID infections? Hospital workers offer a hint
Kozlov M. Nature, Nov 11, 2021.
EVENTS / TRAINING / WEB RESOURCES
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An Open Repository of Real-Time COVID-19 Indicators
Reinhart A, et al. medRxiv, Nov 11, 2021. -
The United States COVID-19 Forecast Hub dataset
Cramer EY, et al. medRxiv, Nov 4, 2021. -
SARS-CoV-2 variants of concern and variants under investigation in England: Technical briefing 28
UK Health Security Agency, Nov 12, 2021. -
The experience of teaching introductory programming skills to bioscientists in Brazil.
Zuvanov Luíza et al. PLoS computational biology 2021 11 (11) e1009534 -
New CDC Partnerships to Advance the Development and Validation of Next Generation Sequencing Tests: A Publicly Available List of Expert Curated Variants
(blog post) Kalman LV. OGPPH, CDC. Nov 16, 2021.
CONCEPTS / COMMENTS
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Antibiotic resistance in the environment
Larsson DGJ, Flach CF. Nat Microbiol, Nov 4, 2021. -
Dissecting the early COVID-19 cases in Wuhan
Worobey M. Science, Nov 18, 2021. -
Understanding Breakthrough Infections Following mRNA SARS-CoV-2 Vaccination.
Klompas Michael et al. JAMA 2021 11 -
The Future of SARS-CoV-2 Vaccination - Lessons from Influenza
Monto AS, et al. New Engl J Med, Nov 11, 2021. -
Patient-focused pathogen genetic counselling-has the time come?
Ferdinand AS, et al. Genome Med. 2021 Nov 8;13(1):178. -
The role of epidemiologists in communicating SARS-CoV-2 evidence: a call for adopting standards.
Smith Meredith Y et al. International journal of epidemiology 2021 6 (5) 1410-1415 -
An mRNA-based anti-tick vaccine catches ticks red-handed
Kopacek P, et al. Sci Transl Med, Nov 17, 2021.
METHODS / TOOLS
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Nanopore sequencing technology, bioinformatics and applications.
Wang Yunhao et al. Nature biotechnology 2021 11 (11) 1348-1365 -
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification.
Schwengers Oliver et al. Microbial genomics 2021 11 (11) -
Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations.
Bogaerts Bert et al. Microbial genomics 2021 11 (11)
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Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences.
Blackwell Grace A et al. PLoS biology 2021 11 (11) e3001421 -
Ten simple rules on writing clean and reliable open-source scientific software.
Hunter-Zinck Haley et al. PLoS computational biology 2021 11 (11) e1009481 -
Accurate long-read de novo assembly evaluation with Inspector
Chen Y, et al. Genome Biol. 2021 Nov 14;22(1):312. -
Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures.
Neubert Kerstin et al. BMC genomics 2021 11 (1) 822 -
A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids.
Urhan Aysun et al. Microbial genomics 2021 11 (11) -
Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time.
Simões Alexandra Sofia et al. Acta medica portuguesa 2021 11
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Bacterial genomic epidemiology with mixed samples.
Mäklin Tommi et al. Microbial genomics 2021 11 (11) -
Using Deep Learning Sequence Models to Identify SARS-CoV-2 Divergence
Ding Y, et al. arXiv, Nov 12, 2021. -
External quality assessment of SARS-CoV-2-sequencing: An ESGMD-SSM pilot trial across 15 European laboratories.
Wegner Fanny et al. Journal of clinical microbiology 2021 11 JCM0169821
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Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens.
Kuchinski Kevin S et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 11
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Development and evaluation of a ligation-free sequence-independent, single-primer amplification (LF-SISPA) assay for whole genome characterization of viruses.
Jothikumar Narayanan et al. Journal of virological methods 2021 11 114346 -
Using neural networks to support high-quality evidence mapping
Rost TB, et al. BMC Bioinformatics. 2021 Oct 21;22(Suppl 11):496.
EVOLUTION / ECOLOGY / POPULATIONS
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Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain.
Haendiges Julie et al. PloS one 2021 11 (11) e0259471 -
Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis.
Zheng Hongyuan et al. Microbial genomics 2021 11 (11) -
Complete Genome Sequence of Rickettsia parkeri Strain Black Gap.
Karpathy Sandor E et al. Microbiology resource announcements 2021 11 (44) e0062321
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Genome structural variation in Escherichia coli O157:H7.
Fitzgerald Stephen F et al. Microbial genomics 2021 11 (11) -
The Population Genetics, Virulence, and Public Health Concerns of Escherichia coli Collected From Rats Within an Urban Environment.
Pettengill J B et al. Frontiers in microbiology 2021 11 631761 -
Evolutionary and Phenotypic Characterization of Two Spike Mutations in European Lineage 20E of SARS-CoV-2.
Ruiz-Rodriguez Paula et al. mBio 2021 11 e0231521 -
A novel SARS-CoV-2 related coronavirus in bats from Cambodia.
Delaune Deborah et al. Nature communications 2021 11 (1) 6563 -
Genomic landscape of SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin
Perico CP, et al. medRxiv, Nov 10, 2021. -
An Opportunistic Survey Reveals an Unexpected Coronavirus Diversity Hotspot in North America.
Hon S Ip et al. Viruses 2021 10 (10)
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The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks.
Peng Min-Sheng et al. Zoological research 2021 11 (6) 833-843 -
Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection.
Zekri Abdel-Rahman N et al. Scientific reports 2021 11 (1) 21632 -
Molecular Evolution and Genomic Characteristics of Genotype H1 of Measles Virus.
Song Jinhua et al. Journal of medical virology 2021 11 -
Molecular Epidemiology of Hepatitis B Virus Genotypes and Subgenotypes in Ethnic Minority Populations, Yunnan Province, China.
Dong Zhe et al. Epidemiology and infection 2021 11 1-20 -
Temporal and gene reassortment analysis of influenza C outbreaks in Hong Kong SAR, China.
Daniels Rodney S et al. Journal of virology 2021 11 JVI0192821 -
Ancestral sequence reconstruction pinpoints adaptations that enable avian influenza virus transmission in pigs
Su W, et al. Nat Microbiol. 2021 Nov;6(11):1455-1465. -
Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveals expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions.
Baptista Rodrigo P et al. Genome research 2021 11
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Clinical outcomes and bacterial characteristics of carbapenem-resistant Klebsiella pneumoniae complex among patients from different global regions (CRACKLE-2): a prospective, multicentre, cohort study.
Wang Minggui et al. The Lancet. Infectious diseases 2021 11 -
Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa.
Ragheb Suzan Mohammed et al. Annals of the New York Academy of Sciences 2021 11
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The antimicrobial resistance landscape of Neisseria gonorrhoeae in New Zealand from November 2018 to March 2019 and the role of sexual orientation in transmission.
Straub Christina et al. Microbial genomics 2021 11 (11) -
Ecology and evolution of antibiotic persistence.
Verstraete L et al. Trends in microbiology 2021 11 -
Genomic Characterization of Group A Streptococci Causing Pharyngitis and Invasive Disease in Colorado, USA, June 2016 - April 2017.
Li Yuan et al. The Journal of infectious diseases 2021 11
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An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms.
Eckstrand Chrissy D et al. PLoS pathogens 2021 11 (11) e1009952 -
Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles.
Syed Abdullah M et al. Science (New York, N.Y.) 2021 11 eabl6184 -
Delta variants of SARS-CoV-2 cause significantly increased vaccine breakthrough COVID-19 cases in Houston, Texas
Christensen PA, et al. Am J Pathol. 2021 Nov 10;S0002-9440(21)00480-6. -
Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption.
Ren Wenlin et al. PLoS pathogens 2021 11 (11) e1010053 -
HIV-1 drug resistance among individuals who seroconverted in the ASPIRE dapivirine ring trial.
Parikh Urvi M et al. Journal of the International AIDS Society 2021 11 (11) e25833 -
Application of Machine Learning Classifier to Candida auris Drug Resistance Analysis
Li D, et al. Front Cell Infect Microbiol. 2021 Oct 15;11:742062. -
Absence of Plasmodium falciparum artemisinin resistance gene mutations eleven years after the adoption of artemisinin-based combination therapy in Nigeria.
Ikegbunam Moses et al. Malaria journal 2021 11 (1) 434 -
Efficacy of artesunate-amodiaquine and artemether-lumefantrine for uncomplicated Plasmodium falciparum malaria in Madagascar, 2018.
Dentinger Catherine M et al. Malaria journal 2021 11 (1) 432
DETECTION / DIAGNOSIS
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Comparison of Whole Genome Sequencing and Repetitive Element PCR for Multidrug- Resistant Pseudomonas aeruginosa Strain Typing.
Spinler Jennifer K et al. The Journal of molecular diagnostics : JMD 2021 11 -
Need for caution when interpreting Xpert MTB/RIF results for rifampin resistance among children.
Murithi W et al. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2021 10 (11) 911-916
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Cold traps as reliable devices for quantitative determination of SARS-CoV-2 load in aerosols.
Gehrke Sven G et al. Environmental monitoring and assessment 2021 11 (12) 778 -
Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units
Charalampous T, et al. Genome Med. 2021 Nov 17;13(1):182. -
RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity
Yaniv K, et al. Water Res. 2021 Oct 28;207:117808.
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Reducing false-positive SARS-CoV-2 diagnoses using long-range RT-qPCR
te Velthuis AJ, et al. medRxiv, Nov 15, 2021.
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A novel wastewater-based epidemiology indexing method predicts SARS-CoV-2 disease prevalence across treatment facilities in metropolitan and regional populations.
Melvin Richard G et al. Scientific reports 2021 11 (1) 21368 -
Early Adoption of Longitudinal Surveillance for SARS-CoV-2 among Staff in Long-Term Care Facilities: Prevalence, Virologic and Sequence Analysis.
Gallichotte Emily N et al. Microbiology spectrum 2021 11 e0100321
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Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia.
Fares Wasfi et al. Microbiology spectrum 2021 11 e0063921 -
SARS-CoV-2 Variants with T135I Nucleocapsid Mutations may Affect Antigen Test Performance.
Jian Ming-Jr et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 11
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CRISPR-Cas12a-Based Detection for the Major SARS-CoV-2 Variants of Concern.
Liang Yuanhao et al. Microbiology spectrum 2021 11 e0101721 -
Streamlined Whole-Genome Sequencing of Mumps Virus for High-Resolution Outbreak Analysis.
Patrick Bryant et al. J Clin Microbiol 2021 11 (1) e0084121 -
Development and Evaluation of a TaqMan Real-Time PCR Assay for the Rapid Detection of Cross-Contamination of RD (Human) and L20B (Mouse) Cell Lines Used in Poliovirus Surveillance.
Ahmad Ausaf et al. Journal of virological methods 2021 11 114354
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Development of a Real-Time Reverse Transcription-PCR Assay To Detect and Quantify Group A Rotavirus Equine-Like G3 Strains.
Katz Eric M et al. Journal of clinical microbiology 2021 8 (11) e0260220
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First human infection of avian influenza A(H5N6) virus reported in Lao People's Democratic Republic, February-March 2021.
Sengkeopraseuth Bounthanom et al. Influenza and other respiratory viruses 2021 11
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Assessing an Adaptation of the Universal Parasite Diagnostic Assay for Bloodborne Parasites in a US State Public Health Laboratory.
Brooke Clemons et al. Am J Trop Med Hyg 2021 11 (2) 671-677
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Strongyloides genotyping: a review of methods and application in public health and population genetics.
Bradbury Richard S et al. International journal for parasitology 2021 11
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Development of a Multiplex Bead Assay To Detect Immunoglobulin G Antibodies to Babesia duncani in Human Serum.
Wang Yong et al. Journal of clinical microbiology 2021 8 (11) e0045821
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An unwanted companion reaches the country: the first record of the alien mosquito Aedes japonicus japonicus (Theobald, 1901) in Slovakia
Cabanova V, et al. Parasit Vectors. 2021 Nov 12;14(1):572.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Transmission patterns of a Mycobacterium avium subsp. paratuberculosis clone within a single heard investigated by Whole Genome Sequencing.
Bolzoni L et al. Veterinary microbiology 2021 11 109272 -
A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital.
Marbjerg Lis et al. Frontiers in medicine 2021 11 733676 -
Genomic epidemiology reveals the reduction of the introduction and spread of SARS-CoV-2 after implementing control strategies in Republic of Korea, 2020.
Kwon Jung-Hoon et al. Virus evolution 2021 11 (2) veab077 -
Changing predominant SARS-CoV-2 lineages drives successive COVID-19 waves in Malaysia, February 2020 to March 2021.
Sam I-Ching et al. Journal of medical virology 2021 11 -
Management of a large outbreak of COVID-19 at a British Army training centre: lessons for the future.
Routledge Matthew et al. BMJ military health 2021 11
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Infection, recovery and re-infection of farmed mink with SARS-CoV-2.
Rasmussen Thomas Bruun et al. PLoS pathogens 2021 11 (11) e1010068 -
Infection, recovery and re-infection of farmed mink with SARS-CoV-2
Rasmussen TB, et al. PLoS Pathog. 2021 Nov 15;17(11):e1010068. -
Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection
Takenouchi T, et al. J Hosp Infect. 2020 Oct 24;107:40-44. -
SARS-CoV-2 Delta vaccine breakthrough transmissibility in Alachua, Florida
Magalis BR, et al. medRxiv, Nov 11, 2021.
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Postvaccination SARS-COV-2 among Health Care Workers in New Jersey: A Genomic Epidemiological Study.
Mathema Barun et al. Microbiology spectrum 2021 11 e0188221
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Survey of pretreatment HIV drug resistance and the genetic transmission networks among HIV-positive individuals in southwestern China, 2014-2020
Xu X, et al. BMC Infect Dis. 2021 Nov 12;21(1):1153.
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Concordance of HIV transmission risk factors elucidated using viral diversification rate and phylogenetic clustering.
McLaughlin Angela et al. Evolution, medicine, and public health 2021 11 (1) 338-348 -
Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020.
Dávila-Conn Vanessa et al. Journal of the International AIDS Society 2021 11 (11) e25836
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Serogroup B meningococcal disease in persons previously vaccinated with a serogroup B meningococcal vaccine - United States, 2014-2019.
Heather E Reese et al. Vaccine 2021 11 (52) 7655-7660
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Reactogenicity within 2 weeks after mRNA COVID-19 vaccines: Findings from the CDC v-safe surveillance system.
Chapin-Bardales Johanna et al. Vaccine 2021 11
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Association Between mRNA Vaccination and COVID-19 Hospitalization and Disease Severity.
Tenforde Mark W et al. JAMA 2021 11
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Myocarditis After mRNA-1273 Vaccination: A Population-Based Analysis of 151 Million Vaccine Recipients Worldwide
Straus W, et al. medRxiv, Nov 12, 2021.
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Evaluation of the BNT162b2 Covid-19 Vaccine in Children 5 to 11 Years of Age.
Walter Emmanuel B et al. The New England journal of medicine 2021 11 -
mRNA vaccination induces tick resistance and prevents transmission of the Lyme disease agent
Sajid A, et al. Sci Transl Med, Nov 17, 2021.
HOST-MICROBE INTERACTIONS
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Mapping the human genetic architecture of COVID-19: an update
COVID-19 Host Genetics Initiative, Ganna A. medRxiv, Nov 11, 2021. -
From online data collection to identification of disease mechanisms: The IL-1beta, IL-6 and TNF-alpha cytokine triad is associated with post-acute sequelae of COVID-19 in a digital research cohort
Schultheiss C, et al. medRxiv, Nov 16, 2021. -
Predicting the zoonotic capacity of mammals to transmit SARS-CoV-2.
Fischhoff Ilya R et al. Proceedings. Biological sciences 2021 11 (1963) 20211651 -
Prediction of SARS-CoV-2 hosts among Brazilian mammals and new coronavirus transmission chain using evolutionary bioinformatics.
Lopes Luciano Rodrigo et al. Animal diseases 2021 11 (1) 20 -
Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus.
Downes Damien J et al. Nature genetics 2021 11 (11) 1606-1615 -
Molecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
McCallum Matthew et al. Science (New York, N.Y.) 2021 11 eabl8506
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.
- Page last reviewed:Feb 1, 2024
- Page last updated:Jan 16, 2025