Advanced Molecular Detection Clips Content (Published on 06/03/2021)
NEWS
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Wanted: rules for pandemic data access that everyone can trust
(editorial) Nature, Jun 1, 2021. -
The next pandemic is already happening--targeted disease surveillance can help prevent it
Miller M. The Conversation, Jun 1, 2021. -
Covid-19: Variants are spreading in countries with low vaccination rates
Dyer O. BMJ, 2021; 373. -
Coronavirus variants get Greek names--but will scientists use them?
Callaway E. Nature, Jun 1, 2021. -
India's COVID crisis flags need to forecast variants
Agrawal A. Nature, Jun 1, 2021. -
Two more coronaviruses may infect people
King A. Science, May 28, 2021. -
A pandemic upside: The flu virus became less diverse, simplifying the task of making flu shots
Branswell H. STAT, Jun 2, 2021. -
After COVID-19 successes, researchers push to develop mRNA vaccines for other diseases
May M. Nat Med, May 31, 2021. -
JHU Researchers Develop 15-Minute PCR System, Drug-Resistant Gonorrhea Test
Johnson M. GenomeWeb, May 28, 2021. -
Global Subway Metagenomics Study Reveals Cities' Microbial Fingerprints
GenomeWeb, May 28, 2021.
CONCEPTS / COMMENTS
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Next-generation microbiology: from comparative genomics to gene function.
Kobras Carolin M et al. Genome biology 2021 5 (1) 123 -
Framing Bacterial Genomics for Public Health(care).
Halpin Alison Laufer et al. Journal of clinical microbiology 2021 6 JCM0013521
METHODS / TOOLS
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ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.
Pavlovikj Natasha et al. PeerJ 2021 6 e11376 -
Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine.
Gu Qiang et al. PLoS computational biology 2021 6 (6) e1009014 -
Leveraging pathogen sequence and contact tracing data to enhance vaccine trials in emerging epidemics.
Kahn Rebecca et al. Epidemiology (Cambridge, Mass.) 2021 5 -
Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads.
Commichaux Seth et al. BMC genomics 2021 5 (1) 389 -
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.
Harrison Peter W et al. Nucleic acids research 2021 5 -
Mathematical modelling and phylodynamics for the study of dog rabies dynamics and control: A scoping review.
Layan Maylis et al. PLoS neglected tropical diseases 2021 5 (5) e0009449 -
An Unsupervised Algorithm for Host Identification in Flaviviruses.
Truong Nguyen Phuoc et al. Life (Basel, Switzerland) 2021 6 (5) -
The CDC HIV Outbreak Coordination Unit: Developing a Standardized, Collaborative Approach to HIV Outbreak Assessment and Response.
Oster Alexandra M et al. Public health reports (Washington, D.C. : 1974) 2021 5 333549211018678
EVOLUTION / ECOLOGY / POPULATIONS
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A global metagenomic map of urban microbiomes and antimicrobial resistance.
Danko David et al. Cell 2021 5 -
Campylobacter jejuni ST50, a pathogen of global importance: A comparative genomic analysis of isolates from Australia, Europe and North America.
Wallace Rhiannon L et al. Zoonoses and public health 2021 5 -
A human respiratory tract-associated bacterium with an extremely small genome.
Fukuda Kazumasa et al. Communications biology 2021 5 (1) 628 -
A Peek into the Plasmidome of Global Sewage.
Kirstahler Philipp et al. mSystems 2021 6 e0028321 -
Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family.
Wang Chen et al. Bioinformatics (Oxford, England) 2021 5 -
Genome-wide analysis of SARS-CoV-2 in VietnamGenome-wide analysis of SARS-CoV-2 strains circulating in Vietnam: understanding the nature of the epidemic and role of the D614G mutation.
Dao Manh H et al. Journal of medical virology 2021 5 -
Analysis of SARS-CoV-2 mutations reveals three types of temporal dynamics and one is correlated with international travels
Arevalo SJ. bioRxiv, Jun 1, 2021. -
E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil.
Ferrareze Patrícia Aline Gröhs et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 5 104941 -
Emergence of a new SARS-CoV-2 variant from GR clade with a novel S glycoprotein mutation V1230L in West Bengal, India
Sarkar R, et al. medRxiv, May 26, 2021. -
SARS-CoV-2 variants of concern are emerging in India.
Singh Jasdeep et al. Nature medicine 2021 5 -
Exploring the natural origins of SARS-CoV-2 in the light of recombination
Lytras S, et al. bioRxiv, May 27, 2021. -
Whole gene analysis of a genotype G29P[6] human rotavirus strain identified in Central African Republic.
Banga-Mingo Virginie et al. BMC research notes 2021 6 (1) 218 -
Comparative analysis of spatial-temporal patterns of human metapneumovirus and respiratory syncytial virus in Africa using genetic data, 2011-2014.
Oketch John W et al. Virology journal 2021 5 (1) 104 -
Subtype distribution of zoonotic pathogen Cryptosporidium felis in humans and animals in several countries.
Jiang Wen et al. Emerging microbes & infections 2020 10 (1) 2446-2454 -
Detection and genetic characterisation of Toxoplasma gondii circulating in free-range chickens, pigs and seropositive pregnant women in Benue state, Nigeria.
Nzelu Ifeoma N et al. PLoS neglected tropical diseases 2021 6 (6) e0009458 -
Low genetic variation in Echinococcus multilocularis from the Western Sichuan Plateau of China revealed by microsatellite and mitochondrial DNA markers.
Shang Jing-Ye et al. Acta tropica 2021 6 105989
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden.
Karlsson Philip A et al. Frontiers in microbiology 2021 6 664665 -
Risk factors for acquisition of colistin-resistant Klebsiella pneumoniae and expansion of a colistin-resistant ST307 epidemic clone in hospitals in Marseille, France, 2014 to 2017.
Baron Sophie Alexandra et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 5 (21) -
Genetic factors involved in fosfomycin resistance of multidrug-resistant Acinetobacter baumannii.
Leite Gleice C et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 5 104943 -
SARS-CoV-2 variants, spike mutations and immune escape.
Harvey William T et al. Nature reviews. Microbiology 2021 6 -
Clinical outcomes in COVID-19 patients infected with different SARS-cov-2 variants in marseille, France.
Dao Thi Loi et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2021 5 -
SARS-CoV-2 genomic surveillance identifies naturally occurring truncation of ORF7a that limits immune suppression.
Nemudryi Artem et al. Cell reports 2021 5 (9) 109197 -
Differential disease severity and whole-genome sequence analysis for human influenza A/H1N1pdm virus in 2015-2016 influenza season.
Liu Hsuan et al. Virus evolution 2021 5 (1) veab044 -
Favipiravir-resistant influenza A virus shows potential for transmission.
Goldhill Daniel H et al. PLoS pathogens 2021 6 (6) e1008937 -
Molecular Features of the Measles Virus Viral Fusion Complex That Favor Infection and Spread in the Brain.
Mathieu Cyrille et al. mBio 2021 6 e0079921 -
Emergence of Human Immunodeficiency Virus-1 Drug Resistance During the 3-Month World Health Organization-Recommended Enhanced Adherence Counseling Period in the CART-1 Cohort Study.
Brown Jennifer A et al. Open forum infectious diseases 2021 5 (5) ofab046
DETECTION / DIAGNOSIS
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CRISPR diagnostics.
Abudayyeh Omar O et al. Science (New York, N.Y.) 2021 5 (6545) 914-915 -
Feasibility of neighborhood and building scale wastewater-based genomic epidemiology for pathogen surveillance.
Spurbeck Rachel R et al. The Science of the total environment 2021 5 147829 -
Identification of tick-borne pathogens by metagenomic next-generation sequencing in Dermacentor nuttalli and Ixodes persulcatus in Inner Mongolia, China.
Jiao Jun et al. Parasites & vectors 2021 5 (1) 287 -
Clinical Evaluation of an Improved Metagenomic Next-Generation Sequencing Test for the Diagnosis of Bloodstream Infections.
Jing Chendi et al. Clinical chemistry 2021 6 -
On-Site Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria in Cambodia With Portable Laboratory Equipment.
Hirabayashi Aki et al. Frontiers in microbiology 2021 6 675463 -
Evaluation of Metagenomic-Enabled Antibiotic Resistance Surveillance at a Conventional Wastewater Treatment Plant.
Majeed Haniyyah J et al. Frontiers in microbiology 2021 6 657954 -
Minipool testing for SARS-CoV-2 RNA in United States blood donors.
Bakkour Sonia et al. Transfusion 2021 5 -
Wastewater-Based Epidemiology as an Early Warning System for the Spreading of SARS-CoV-2 and Its Mutations in the Population.
Mackulak Tomáš et al. International journal of environmental research and public health 2021 6 (11) -
Clinical validation of colorimetric RT-LAMP, a fast, highly sensitive and specific COVID-19 molecular diagnostic tool that is robust to detect SARS-CoV-2 variants of concern
Alves PA, et al. medRxiv, Jun 2, 2021. -
Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater
Lin X, et al. medRxiv, May 29, 2021. -
Monitoring emergence of SARS-CoV-2 B.1.1.7 Variant through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19) from December 2020 to March 2021
Carcereny A, et al. medRxiv, May 30, 2021. -
COVID-19 mass testing: harnessing the power of wastewater epidemiology
Fitzgerald SF, et al. medRxiv, May 26, 2021. -
Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK.
Hillary Luke S et al. Water research 2021 6 117214 -
Severe Acute Respiratory Syndrome Coronavirus 2: The Emergence of Important Genetic Variants and Testing Options for Clinical Laboratories
Buchan BW, Yan JD. Clin Microbiol Newsletter, Jun 1, 2021. -
Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea.
Park Kyungmin et al. Viruses 2021 6 (5) -
Surveillance for Babesia odocoilei in Hunter-Harvested Wild-Elk (Cervus elaphus canadensis) from Pennsylvania, USA (2016-2017).
Calvente Elizabeth Jean et al. Veterinary sciences 2021 6 (6) -
Detection of Babesia odocoilei in Humans with Babesiosis Symptoms.
Scott John D et al. Diagnostics (Basel, Switzerland) 2021 6 (6) -
A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus.
Makunin Alex et al. Molecular ecology resources 2021 5 -
Laboratory Detection of Malaria Antigens: a Strong Tool for Malaria Research, Diagnosis, and Epidemiology.
Plucinski Mateusz et al. Clinical microbiology reviews 2021 5 e0025020 -
Genetic diversity analysis of Chinese Leishmania isolates and development of L. donovani complex-specific markers by RAPD.
Yuan Dongmei et al. BMC infectious diseases 2021 5 (1) 464
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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The Genomic Epidemiology of Carbapenemase-Producing Enterobacterales (CPE) at a Hospital System in Toronto, Ontario, Canada, 2007-2018.
Jamal Alainna J et al. Antimicrobial agents and chemotherapy 2021 6 AAC0036021 -
The largest prison outbreak of TB in Western Europe investigated using whole-genome sequencing.
Roycroft E et al. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2021 5 (6) 491-497 -
Outbreak investigation of SARS-CoV-2 transmission in an emergency childcare centre.
Soto Julio C et al. Canadian journal of public health = Revue canadienne de sante publique 2021 5 -
Applying Genomic Epidemiology to Characterize a COVID-19 Outbreak in a Developmentally Disabled Adult Group Home Setting, Arizona.
Yaglom Hayley D et al. Frontiers in public health 2021 6 668214 -
Molecular epidemiology of SARS-CoV-2 isolated from COVID-19 family clusters.
Gunadi et al. BMC medical genomics 2021 6 (1) 144 -
SARS-CoV-2 Infections and Viral Isolations among Serially Tested Cats and Dogs in Households with Infected Owners in Texas, USA.
Hamer Sarah A et al. Viruses 2021 6 (5) -
Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control.
Bbosa Nicholas et al. Viruses 2021 6 (6) -
Phylogenetic evidence of HIV-1 transmission linkage between two men who have sex with men.
Zhang Jiafeng et al. Virology journal 2021 6 (1) 106
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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COVID-19 Vaccine Breakthrough Infections Reported to CDC - United States, January 1-April 30, 2021.
et al. MMWR. Morbidity and mortality weekly report 2021 5 (21) 792-793 -
BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans.
Sahin Ugur et al. Nature 2021 5 -
Effectiveness of COVID-19 vaccines against the B.1.617.2 variant
Bernal JL, et al. Public Health England (preprint), May 24, 2021. -
Selecting and Using the Appropriate Influenza Vaccine for Each Individual.
Sekiya Toshiki et al. Viruses 2021 6 (6)
HOST-MICROBE INTERACTIONS
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A next generation sequencing combined genome-wide association study identifies novel tuberculosis susceptibility loci in Chinese population.
Li Mo et al. Genomics 2021 5 -
Predictive nomogram for leprosy using genetic and epidemiological risk factors in Southwestern China: Case-control and prospective analyses.
Long Si-Yu et al. EBioMedicine 2021 5 103408 -
Extremes of age are associated with differences in the expression of selected pattern recognition receptor genes and ACE2, the receptor for SARS-CoV-2: implications for the epidemiology of COVID-19 disease.
Bickler Stephen W et al. BMC medical genomics 2021 5 (1) 138 -
Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19.
Povysil Gundula et al. The Journal of clinical investigation 2021 5 -
Longitudinal immune dynamics of mild COVID-19 define signatures of recovery and persistence
Talla A, et al. bioRxiv, May 26, 2021. -
Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation
Lee HK, et al. medRxiv, May 30, 2021. -
Blood DNA methylation and COVID-19 outcomes.
Balnis Joseph et al. Clinical epigenetics 2021 5 (1) 118 -
SARS-CoV-2 variants of concern partially escape humoral but not T-cell responses in COVID-19 convalescent donors and vaccinees.
Geers Daryl et al. Science immunology 2021 5 (59) -
Genetics of symptom remission in outpatients with COVID-19.
Dubé Marie-Pierre et al. Scientific reports 2021 5 (1) 10847 -
The UGT2A1/UGT2A2 locus is associated with COVID-19-related anosmia
Shelton JF, et al. medRxiv, May 31, 2021. -
Increased hepatitis B virus quasispecies diversity is correlated with liver fibrosis progression.
Wu Hongkai et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 5 104938 -
Taxonomic signatures of cause-specific mortality risk in human gut microbiome.
Salosensaari Aaro et al. Nature communications 2021 5 (1) 2671


Disclaimer: Articles listed in the Advanced Molecular Detection Clips are selected by the CDC Office of Genomics and Precision Public Health 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:Oct 1, 2023
- Page last updated:Nov 16, 2023
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