Advanced Molecular Detection Clips Content (Published on 04/30/2021)
NEWS
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One million coronavirus sequences: popular genome site hits mega milestone.
Maxmen Amy et al. Nature 2021 4 -
How blackouts, fires, and a pandemic are driving shortages of pipette tips--and hobbling science
Sheridan K. STAT, Apr 28, 2021. -
COVID-19 variants spread faster but grew milder over time in Ohio
Van Beusekom M. CIDRAP, Apr 27, 2021. -
New Covid variant detected at Texas A&M lab shows signs of antibody resistance and more severe illness in young people
Mendez R. CNBC, Apr 22, 2021. -
India's surge leads to further global COVID rise as role of variants probed
Schnirring L. CIDRAP, Apr 28, 2021. -
Could a souped-up version of existing Covid-19 tests be our shortcut to tracking variants?
Renault M. STAT, Apr 23, 2021. -
Vaccines Are Effective Against the New York Variant, Studies Find
Mandavilli A. New York Times, Apr 22, 2021. -
COVID-19 vaccine responses to be studied in people with immune deficits
NIH, Apr 23, 2021. -
23andMe Team Sees Genetic, Nongenetic Contributors to COVID-19 Risk in Trans-Ancestry Study
GenomeWeb, Apr 22, 2021. -
COVID-19 Severity Linked to mRNA, lncRNA Signature in Blood
GenomeWeb, Apr 23, 2021. -
Malaria vaccine shows promise--now come tougher trials
Ledford H. Nature, Apr 26, 2021. -
Genetically modified mosquitoes to be released in Florida after years of planning
Fitzsimons T. NBC, Apr 27, 2021.
CONCEPTS / COMMENTS
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Spatial infectious disease epidemiology: on the cusp.
Chowell G et al. BMC medicine 2018 10 (1) 192 -
Emergence of New Disease: How Can Artificial Intelligence Help?
Park Yurim et al. Trends in molecular medicine 2020 5 (7) 627-629 -
Individuals cannot rely on COVID-19 herd immunity: Durable immunity to viral disease is limited to viruses with obligate viremic spread.
Yewdell Jonathan W et al. PLoS pathogens 2021 4 (4) e1009509 -
SARS-CoV-2 vaccination efficacy on hospitalisation and variants.
Rozencwajg Sacha et al. Anaesthesia, critical care & pain medicine 2021 4 100867 -
ZTCG: Viruses expand the genetic alphabet
Grome MW, Isaacs FJ. Science, Apr 30, 2021. -
Real-World Ethical Dilemmas in Laboratory Safety for Microbiology Under-Resourced and Outreach Teaching.
Smith-Keiling Beverly L et al. Frontiers in microbiology 2021 4 589569
METHODS / TOOLS
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Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation.
Ferreira Fabienne Antunes et al. Microbial genomics 2021 4 (4)
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Haplotype Explorer: an infection cluster visualization tool for spatiotemporal dissection of the COVID-19 pandemic.
Kawano-Sugaya Tetsuro et al. G3 (Bethesda, Md.) 2021 4
EVOLUTION / ECOLOGY / POPULATIONS
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Environmental dissemination of pathogenic Listeria monocytogenes in flowing surface waters in Switzerland.
Raschle Susanne et al. Scientific reports 2021 4 (1) 9066 -
Genomic and epidemiological characteristics of SARS-CoV-2 in Africa.
Lamptey Jones et al. PLoS neglected tropical diseases 2021 4 (4) e0009335 -
SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation.
Mora Jose Arturo Molina et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 4 104872 -
Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
West AP Jr, et al. bioRxiv, Apr 22, 2021. -
Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India
Cherian S, et al. bioRxiv, Apr 24, 2021. -
First Report on the Latvian SARS-CoV-2 Isolate Genetic Diversity.
Zrelovs Nikita et al. Frontiers in medicine 2021 4 626000 -
Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021.
Funk Tjede et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 4 (16) -
Global and local mutations in Bangladeshi SARS-CoV-2 genomes.
Hasan Md Mahbub et al. Virus research 2021 3 198390 -
Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants of potential concern
Garushyants SK, et al. bioRxiv, Apr 26, 2021. -
Contrasting epidemiology and population genetics of COVID-19 infections defined with 74 polymorphic loci in SARS-CoV-2 genomes sampled globally.
Chan F, et al. medRxiv, Apr 26, 2021. -
Transmission dynamics of the rubella virus circulating in China during 2010-2019: two lineage switches between genotypes 1E and 2B.
Zhu Zhen et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
Molecular investigation of the dengue outbreak in Karnataka, South India, reveals co-circulation of all four dengue virus serotypes.
Rai Praveen et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 4 104880 -
Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay.
Gräf Tiago et al. Emerging infectious diseases 2021 4 (5) 1393-1404 -
Metagenomic sequencing reveals viral abundance and diversity in mosquitoes from the Shaanxi-Gansu-Ningxia region, China.
He Xiaozhou et al. PLoS neglected tropical diseases 2021 4 (4) e0009381
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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A novel mechanism of streptomycin resistance in Yersinia pestis: Mutation in the rpsL gene.
Dai Ruixia et al. PLoS neglected tropical diseases 2021 4 (4) e0009324 -
Emergence of additional drug resistance during treatment of multidrug-resistant tuberculosis in China: a prospective cohort study.
Hu Yi et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2021 4 -
Ecological niche adaptation of Salmonella Typhimurium U288 is associated with altered pathogenicity and reduced zoonotic potential.
Kirkwood Mark et al. Communications biology 2021 4 (1) 498 -
Haemophilus influenzae one day in Denmark: prevalence, circulating clones, and dismal resistance to aminopenicillins.
Nørskov-Lauritsen Niels et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2021 4 -
Genetic diversity and pathogenic potential of Shiga toxin-producing Escherichia coli (STEC) derived from German flour.
Projahn Michaela et al. International journal of food microbiology 2021 4 109197 -
Acquisition of ciprofloxacin resistance among an expanding clade of β-lactamase positive, serogroup Y Neisseria meningitidis in the United States.
Potts Caelin C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4
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Introduction of ORF3a-Q57H SARS-CoV-2 Variant Causing Fourth Epidemic Wave of COVID-19, Hong Kong, China.
Chu Daniel K W et al. Emerging infectious diseases 2021 4 (5) 1492-1495 -
SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection.
Choudhary Manish C et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
Short Communication: Integrase Strand Transfer Inhibitors Drug Resistance Mutations in Puerto Rico HIV-Positive Individuals.
López Pablo et al. International journal of environmental research and public health 2021 4 (5) -
Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations.
Mokaya Jolynne et al. Journal of viral hepatitis 2021 4 -
Exposure to diverse Plasmodium falciparum genotypes shapes the risk of symptomatic malaria in incident and persistent infections: A longitudinal molecular epidemiologic study in Kenya.
Sumner Kelsey M et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
Common virulence gene expression in adult first-time infected malaria patients and severe cases.
Wichers Jan Stephan et al. eLife 2021 4
DETECTION / DIAGNOSIS
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Genomics reveals the novel species placement of industrial contaminant isolates incorrectly identified as Burkholderia lata
Cunningham-Oakes Edward et al. Microbial genomics 2021 4 (4) -
Detection of Pathogenic Bacteria from Septic Patients Using 16S rRNA gene Targeted Metagenomic Sequencing.
Fida Madiha et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
Metagenomic sequencing as a pathogen-agnostic clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis of diagnostic test accuracy studies
Govender KN, et al. J Clin Microbiol. 2021 Apr 28
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SARS-CoV-2 reinfection caused by the P.1 lineage in Araraquara city, Sao Paulo State, Brazil.
Romano Camila Malta et al. Revista do Instituto de Medicina Tropical de Sao Paulo 2021 4 e36 -
Monitoring SARS-CoV-2 Circulation and Diversity through Community Wastewater Sequencing, the Netherlands and Belgium.
Izquierdo-Lara Ray et al. Emerging infectious diseases 2021 4 (5) 1405-1415 -
Diagnostic accuracy of loop mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations.
Ptasinska Anetta et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2021 4 -
Novel indel mutation in the N gene of SARS-CoV-2 clinical samples that were diagnosed positive in a commercial RT-PCR assay.
Lee Sanghoo et al. Virus research 2021 3 198398 -
Resurgence of SARS-CoV-2: detection by community viral surveillance
Riley S, et al. Science, Apr 23, 2021. -
Resurgence of SARS-CoV-2: detection by community viral surveillance.
Riley Steven et al. Science (New York, N.Y.) 2021 4 -
COV-ID: A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva
Warneford-Thomson R, et al. medRxiv, Apr 23, 2021. -
Global Trends in Norovirus Genotype Distribution among Children with Acute Gastroenteritis.
Cannon Jennifer L et al. Emerging infectious diseases 2021 4 (5) 1438-1445
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Evaluating the diagnostic test accuracy of molecular xenomonitoring methods for characterising community burden of lymphatic filariasis.
Pryce Joseph et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay.
Batson Joshua et al. eLife 2021 4
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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A cluster of Achromobacter xylosoxidans led to identification of Pseudomonas aeruginosa and Serratia marcescens contamination at a long-term-care facility.
Dunne Eileen M et al. American journal of infection control 2021 4
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Outbreak of Shiga toxin-producing Escherichia coli O157 linked with consumption of a fast-food product containing imported cucumbers, United Kingdom, August 2020.
Mulchandani Ranya et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 4
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Yersinia enterocolitica Outbreak Associated with Pasteurized Milk.
Gruber Joann F et al. Foodborne pathogens and disease 2021 4 (7) 448-454
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Linked Clusters of SARS-CoV-2 Variant B.1.351 - Maryland, January-February 2021.
Feder Kenneth A et al. MMWR. Morbidity and mortality weekly report 2021 4 (17) 627-631
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Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity.
Esper Frank P et al. JAMA network open 2021 4 (4) e217746 -
Transmission of SARS-CoV-2 on a Patient Transport Van.
Jones Lucas D et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand.
Geoghegan Jemma L et al. Emerging infectious diseases 2021 4 (5) 1317-1322
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Introduction, Transmission Dynamics, and Fate of Early SARS-CoV-2 Lineages in Santa Clara County, California.
Villarino Elsa et al. The Journal of infectious diseases 2021 4
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Severe Acute Respiratory Syndrome Coronavirus 2 P.2 Lineage Associated with Reinfection Case, Brazil, June-October 2020.
Resende Paola Cristina et al. Emerging infectious diseases 2021 4 (7) -
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.
Giovanetti Marta et al. Communications biology 2021 4 (1) 489 -
Progression and transmission of HIV (PATH 4.0)-A new agent-based evolving network simulation for modeling HIV transmission clusters.
Singh Sonza et al. Mathematical biosciences and engineering : MBE 2021 4 (3) 2150-2181
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Acquisition and transmission of HIV-1 among migrants and Chinese in Guangzhou, China from 2008 to 2012: Phylogenetic analysis of surveillance data.
Yan Huanchang et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 4 104870
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Design of multidrug-resistant tuberculosis treatment regimens based on DNA sequencing.
Grobbel Hans-Peter et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4 -
BNT162b2 Vaccination Effectively Prevents the Rapid Rise of SARS-CoV-2 Variant B.1.1.7 in high risk populations in Israel.
Munitz A et al. Cell reports. Medicine 2021 4 100264
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Genetic mismatch explains sizable variation of COVID-19 vaccine efficacy in clinical trials
Cao L, et al. medRxiv, Apr 23, 2021. -
Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes.
Saad-Roy Chadi M et al. Science (New York, N.Y.) 2021 3 (6540) 363-370
HOST-MICROBE INTERACTIONS
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Trans-ancestry analysis reveals genetic and nongenetic associations with COVID-19 susceptibility and severity
Shelton JF, et al. Nat Genet, Apr 22, 2021. -
Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection
Biering SB, et al. bioRxiv, Apr 23, 2021. -
The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection
McDonald JT, et al. bioRxiv, Apr 23, 2021. -
Immunogenetics of resistance to SARS-CoV-2 infection in discordant couples
Castelli EC, et al. medRxiv, Apr 25, 2021. -
Epigenome-wide association study of COVID-19 severity with respiratory failure.
Castro de Moura Manuel et al. EBioMedicine 2021 4 103339 -
Identification of PBMC-based Molecular Signature Associational with COVID-19 Disease Severity.
Shaath Hibah et al. Heliyon 2021 4 e06866 -
Increased viral variants in children and young adults with impaired humoral immunity and persistent SARS-CoV-2 infection: A consecutive case series
Truong TT, et al. eBiomedicine, Apr 26, 2021. -
The Influence Of Hla Genotype On The Severity Of Covid-19 Infection.
Langton David J et al. HLA 2021 4 -
Genome-Wide B Cell, CD4 +, and CD8 + T Cell Epitopes That Are Highly Conserved between Human and Animal Coronaviruses, Identified from SARS-CoV-2 as Targets for Preemptive Pan-Coronavirus Vaccines
Prakash S, et al. J Immunol. 2021 Apr 28;ji2001438. -
Our Evolving Understanding of Kawasaki Disease Pathogenesis: Role of the Gut Microbiota.
Kaneko Kazunari et al. Frontiers in immunology 2020 8 1616
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 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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