Pathogen Advanced Molecular Detection Database|Archive|Public Health Genomics and Precision Health Knowledge Base (PHGKB)

CONCEPTS / COMMENTS

The viral arms race.
et al. Nature biotechnology 2021 5 (5) 527
Disease surveillance for the COVID-19 era: time for bold changes
Morgan OW, et al. Lancet 2021 May 14;S0140-6736(21)01096-5.
COVID-19 testing turns to T cells
Sheridan C. Nat Biotechnol, 2021;39:533?534.
The Covid-19 Infodemic - Applying the Epidemiologic Model to Counter Misinformation.
Scales David et al. The New England journal of medicine 2021 5
Ten simple rules to cultivate transdisciplinary collaboration in data science.
Sahneh Faryad et al. PLoS computational biology 2021 5 (5) e1008879

METHODS / TOOLS

MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads.
Hallgren Malte B et al. Biology methods & protocols 2021 5 (1) bpab008
A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch.
Argimón Silvia et al. Nature communications 2021 5 (1) 2879
IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome.
Desai Sanket et al. BMC bioinformatics 2021 5 (1) 247
Mass Spectrometry Analytical Responses to the SARS-CoV2 Coronavirus in Review
Griffin JH, Downard KM. Trends Analyt Chem. 2021 May 11;116328.
The Biobanque québécoise de la COVID-19 (BQC19)-A cohort to prospectively study the clinical and biological determinants of COVID-19 clinical trajectories.
Tremblay Karine et al. PloS one 2021 5 (5) e0245031
Integration of sample preparation with RNA-Amplification in a hand-held device for airborne virus detection.
Jiang Xiao et al. Analytica chimica acta 2021 5 338542
Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity after de novo assembly of native full-length hepatitis B virus genomes.
Goldsmith Chloe et al. Microbial genomics 2021 5 (5)

EVOLUTION / ECOLOGY / POPULATIONS

Retrospective whole-genome comparison of Salmonella enterica serovar Enteritidis from foodborne outbreaks in Southern Brazil.

Mascitti Andréa K et al. Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2021 5
No particular genomic features underpin the dramatic economic consequences of 17 century plague epidemics in Italy.

Seguin-Orlando Andaine et al. iScience 2021 5 (4) 102383
Genome-wide insights into population structure and host specificity of Campylobacter jejuni.

Epping Lennard et al. Scientific reports 2021 5 (1) 10358
Mass burial genomics reveals outbreak of enteric paratyphoid fever in the Late Medieval trade city Lubeck

Haller M, et al. iScience. 2021 Apr 20;24(5):102419.
Genetic Diversity of Meningococcal Serogroup B Vaccine Antigens among Carriage Isolates Collected from Students at Three Universities in the United States, 2015-2016.

Marjuki Henju et al. mBio 2021 5 (3)
One year of SARS-CoV-2: Genomic characterization of COVID-19 outbreak in Qatar

Benslimane FM, et al. medRxiv, May 20, 2021.
Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

Okoh OS, et al. medRxiv, May 19, 2021.
Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations

Shen L, et al. medRxiv, May 18, 2021.
Vaccine-escape and fast-growing mutations in the United Kingdom, the United States, Singapore, Spain, India, and other COVID-19-devastated countries.

Wang Rui et al. Genomics 2021 5
Phylogenomics and population genomics of SARS-CoV-2 in Mexico reveals variants of interest (VOI) and a mutation in the Nucleocapsid protein associated with symptomatic versus asymptomatic carriers

Barona-Gomez F, et al. medRxiv, May 18, 2021.
Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020.

Nyunt Myat Htut et al. Scientific reports 2021 5 (1) 10203
Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage.

Colson Philippe et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2021 5
Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018.

Gaye Amy et al. Scientific reports 2021 5 (1) 10321
Live poultry feeding and trading network and the transmission of avian influenza A(H5N6) virus in a large city in China, 2014-2015

Zhang R, et al. Int J Infect Dis. 2021 May 14;S1201-9712(21)00423-9.
Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe

Benschop KS, et al. Emerg Infect Dis, Apr 30, 2021.
Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic

Patrono LV, et al. bioRxiv, May 14, 2021.

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

Genomic Analysis of the Predominant Strains and Antimicrobial Resistance Determinants Within 1479 Neisseria gonorrhoeae Isolates From the US Gonococcal Isolate Surveillance Project in 2018.
Reimche Jennifer L et al. Sexually transmitted diseases 2021 5 (8S) S78-S87
Emergence and Expansion of a Carbapenem-Resistant Pseudomonas aeruginosa Clone Are Associated with Plasmid-Borne bla and Virulence-Related Genes.
Hu Yanyan et al. mSystems 2021 5 (3)
Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant.
Xianding Deng et al. Cell 2021 5 (13) 3426-3437.e8
HIV drug resistance among adults initiating antiretroviral therapy in Uganda
Watera C, et al. J Antimicrob Chemother. 2021 May 15;dkab159.

DETECTION / DIAGNOSIS

Pathogenic potential assessment of the Shiga toxin-producing Escherichia coli by a source attribution-considered machine learning model.
Im Hanhyeok et al. Proceedings of the National Academy of Sciences of the United States of America 2021 5 (20)
Use of different approaches for the culture-independent typing of Mycoplasma pneumoniae from two geographically distinct regions.
Dumke Roger et al. Journal of microbiological methods 2021 5 106239
Etiology of acute meningitis and encephalitis from hospital-based surveillance in South Kazakhstan oblast, February 2017-January 2018.
Bumburidi Yekaterina et al. PloS one 2021 5 (5) e0251494
Using Neisseria meningitidis genomic diversity to inform outbreak strain identification.
Retchless Adam C et al. PLoS pathogens 2021 5 (5) e1009586
Pilot study of a combined genomic and epidemiologic surveillance program for hospital-acquired multidrug-resistant pathogens across multiple hospital networks in Australia.
Sherry Norelle L et al. Infection control and hospital epidemiology 2021 5 (5) 573-581
Mutation-specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation
Wang H, et al. J Clin Microbiol. 2021 May 19;JCM.00926-21.
Evaluating the Presence of Replication-Competent Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) From Nursing Home Residents With Persistently Positive Reverse Transcription Polymerase Chain Reaction (RT-PCR) Results.
Joseph D Lutgring et al. Clin Infect Dis 2021 5 (3) 525-528
Specific Detection of Influenza A and B Viruses by CRISPR-Cas12a-Based Assay.
Park Bum Ju et al. Biosensors 2021 4 (3)

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Regional spread of blaNDM-1-containing Klebsiella pneumoniae ST147 in post-acute care facilities
Lapp Z, et al. Clin Infect Dis. 2021 May 17;ciab457.
Tuberculosis Genotype Clusters and Transmission in the U.S., 2009-2018.
Wortham Jonathan M et al. American journal of preventive medicine 2021 5 (2) 201-208
Brucellosis Outbreak Traced to Commercially Sold Camel Milk through Whole-Genome Sequencing, Israel
Bardenstein S, et al. Emerg Infect Dis, May 10, 2021.
Applying Genomic Epidemiology to Characterize a COVID-19 Outbreak in a Developmentally Disabled Adult Group Home Setting, Arizona
Yaglom H, et al. Front Public Health, May 13, 2021.
Outbreak investigation of symptomatic SARS-COV-2 VOC 202012/01-lineage B.1.1.7 infection in healthcare workers, Italy.
Loconsole Daniela et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2021 5
SARS-CoV-2 Superspread in Fitness Center, Hong Kong, China, March 2021.
Chu Daniel K W et al. Emerging infectious diseases 2021 5 (8)
Spatiotemporal phylodynamics of hepatitis C among people who inject drugs in India.
Clipman Steven J et al. Hepatology (Baltimore, Md.) 2021 5
Precision Tracing of Household Dengue Spread Using Inter- and Intra-Host Viral Variation Data, Kamphaeng Phet, Thailand
Berry IM, et al. Emerg Infect Dis, Apr 30, 2021.

ANTIMICROBIALS / VACCINES / INTERVENTIONS

Durability of mRNA-1273-induced antibodies against SARS-CoV-2 variants
Pegu A, et al. bioRxiv, May 16, 2021.
Infection and vaccine-induced neutralizing antibody responses to the SARS-CoV-2 B.1.617.1 variant
Edara VV, et al. bioRxiv, May 10, 2021.
Pertactin-Deficient Bordetella pertussis, Vaccine-Driven Evolution, and Reemergence of Pertussis
Ma L, et al. Emerg Infect Dis, April 29, 2021.
Global genomic pathogen surveillance to inform vaccine strategies: a decade-long expedition in pneumococcal genomics
Bentley SD, Lo SW. Genome Med, 2021 May 17;13(1):84.
BNT162b2 mRNA vaccination did not prevent an outbreak of SARS COV-2 variant 501Y.V2 in an elderly nursing home but reduced transmission and disease severity.
Bailly Benoit et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 5
Serotype 2 oral poliovirus vaccine (OPV2) choices and the consequences of delaying outbreak response.
Kalkowska Dominika A et al. Vaccine 2021 5

HOST-MICROBE INTERACTIONS

Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes.
Immel Alexander et al. Molecular biology and evolution 2021 5
Immunology Lessons from the SARS-CoV-2 Pandemic.
Yokoyama Wayne M et al. Annual review of immunology 2021 5 v-vii
Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses
Rebendenne A, et al. bioRxiv, May 14, 2021.
HLA-B*15:01 is associated with asymptomatic SARS-CoV-2 infection
Augusto DG, et al. medRxiv, May 17, 2021.
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis.
Ferrarini Mariana G et al. Communications biology 2021 5 (1) 590
ACE2 polymorphism and susceptibility for SARS-CoV-2 infection and severity of COVID-19.
Möhlendick Birte et al. Pharmacogenetics and genomics 2021 5
Discovery of human ACE2 variants with altered recognition by the SARS-CoV-2 spike protein.
Heinzelman Pete et al. PloS one 2021 5 (5) e0251585
Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics.
Kotliar Dylan et al. Cell 2020 11 (5) 1383-1401.e19
Genomic features of humoral immunity support tolerance model in Egyptian rousette bats.
Larson Peter A et al. Cell reports 2021 5 (7) 109140
Contrasting Epidemiology and Genetic Variation of Plasmodium vivax Infecting Duffy Negatives across Africa.
Lo Eugenia et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 5
How Genetics Might Explain the Unusual Link Between Malaria and COVID-19.
Rusmini Marta et al. Frontiers in medicine 2021 5 650231
Vaginal Microbiome Composition in Early Pregnancy and Risk of Spontaneous Preterm and Early Term Birth Among African American Women
Dunlop AL, et al. Front Cell Infect Microbiol. 2021 Apr 29;11:641005.
Host microbiota can facilitate pathogen infection.
Stevens Emily J et al. PLoS pathogens 2021 5 (5) e1009514

Note: 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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Page last reviewed:Feb 1, 2024
Page last updated:Jan 23, 2025

Advanced Molecular Detection Clips Content (Published on 05/20/2021)

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