Advanced Molecular Detection Clips Content (Published on 03/11/2021)
NEWS
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Scientists underestimated the coronavirus--and are racing to keep up with evolution
Johnson CY. Washington Post, Mar 7, 2021. -
We Now Can See a Virus Mutate Like Never Before
Zhang S. Atlantic, Mar 9, 2021. -
UK COVID-19 variant has significantly higher death rate, study finds
Kelland K. Reuters, Mar 10, 2021. -
Multitude of coronavirus variants found in the US--but the threat is unclear
Callaway E. Nature, Mar 5, 2021. -
How travel brought two COVID variants to the U.S., according to the CDC
McMahon S. Washington Post, Mar 5, 2021. -
More Contagious Variant Is Spreading Fast in U.S., Even as Overall Cases Level Off
Leatherby L, Reinhard S. New York Times, Mar 6, 2020. -
What Happens When People Get Infected With 2 Strains of COVID at Once?
Shivkumar M. The Conversation, Mar 4, 2021. -
English health officials say 16 cases of new COVID variant discovered
Reuters, Mar 4, 2021. -
Health Officials Confirm NYC COVID Variant Is More Infectious, Outpacing UK Strain
Yakas B. Gothamist, Mar 10, 2021. -
Covid-19 Took Disease Tests Out of the Lab--And May Keep Them There
Waterman N. The Verge, Mar 10, 2021. -
At AGBT [Advances in Genome Biology and Technology], Two Labs Share SARS-CoV-2 Genomic Surveillance Experience
Karow J. GenomeWeb, Mar 4, 2021. -
Going universal: The search for an all-in-one coronavirus vaccine
Rogers J. CEPI, Mar 1, 2021. -
Inhaled CRISPR Treatment Targets Influenza and SARS-CoV-2 Infections
GEN, Mar 5, 2021. -
The Rockefeller Foundation Releases New Action Plan to Accelerate Development of a National System for Gathering and Sharing Information on SARS-CoV-2 Genomic Variants and Other Pathogens
(press release) Rockefeller Foundation, Mar 8, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Accelerating National Genomic Surveillance
(report) Rockefeller Foundation, Mar 8, 2021. -
Hands-on training about overfitting.
Demšar Janez et al. PLoS computational biology 2021 3 (3) e1008671 -
mRNA COVID-19 Vaccines: An Incredible Feat of Genomic Technology
(blog post) Cono J, et al. Office of Genomics and Precision Public Health/OS/CDC, Mar 5, 2021.
CONCEPTS / COMMENTS
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A new general mechanism of AMR
York A. Nat Rev Microbiol, Mar 2, 2021. -
The State of Microbiome Science at the Intersection of Infectious Diseases and Antimicrobial Resistance.
Ranallo Ryan T et al. The Journal of infectious diseases 2021 3
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Whole-genome sequencing for TB source investigations: principles of ethical precision public health.
Van Rie A et al. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease 2021 3 (3) 222-227 -
New Zealand's science-led response to the SARS-CoV-2 pandemic.
Geoghegan Jemma L et al. Nature immunology 2021 2 (3) 262-263 -
Forecasting the spread of SARS-CoV-2 is inherently ambiguous given the current state of virus research
Koenen M, et al. PLoS One. 2021 Mar 3;16(3):e0245519.
METHODS / TOOLS
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SARS-CoV-2 evolution in animals suggests mechanisms for rapid variant selection
Bashor L, et al. bioRxiv, Mar 9, 2021. -
Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing
Greig David R et al. Microbial genomics 2021 3
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Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing
Bloom JS, et al. medRxiv, Mar 9, 2021. -
seqQscorer: automated quality control of next-generation sequencing data using machine learning.
Albrecht Steffen et al. Genome biology 2021 3 (1) 75 -
TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference.
Sledzieski Samuel et al. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2021 3 119-130 -
Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants.
Riaz Nasir et al. BMC genomics 2021 3 (1) 148
EVOLUTION / ECOLOGY / POPULATIONS
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Complete and Circularized Bacterial Genome Sequence of Gordonia sp. Strain X0973
Gulvik Christopher A et al. Microbiology resource announcements 2021 3 (9)
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Spatial Epidemiology of Salmonellosis in Florida, 2009-2018.
Xiaolong Li et al. Front Public Health 2021 3 603005
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Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil
da Silva Francisco Jr R, et al. Jan 26, 2021. -
Genome sequencing and analysis of an emergent SARS-CoV-2 variant characterized by multiple spike protein mutations detected from the Central Visayas Region of the Philippines
Tablizo FA, et al. medRxiv, Mar 5, 2021. -
Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021.
Gaymard Alexandre et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 3 (9) -
SARS-CoV-2 within-host diversity and transmission
Lythgoe KA, et al. Science, Mar 9, 2021. -
The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape
Martin DP, et al. medRxiv, Mar 5, 2021. -
Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein
Tegally H, et al. Nature, Mar 9, 2021. -
Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Kemp SA, et al. bioRxiv, Mar 8, 2021. -
One year of SARS-CoV-2 evolution.
Wu Aiping et al. Cell host & microbe 2021 3 -
Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses
Zhou H, et al. bioRxiv, Mar 8, 2021. -
Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission.
Sapoval Nicolae et al. Genome research 2021 2 -
Emergence of a Severe Acute Respiratory Syndrome Coronavirus 2 virus variant with novel genomic architecture in Hong Kong.
Tse Herman et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 3 -
The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.
Martin Darren P et al. medRxiv : the preprint server for health sciences 2021 3 -
Use of Nanopore Sequencing to Characterize African Horse Sickness Virus (AHSV) from the African Horse Sickness Outbreak in Thailand in 2020.
Xinyu Toh et al. Transboundary and emerging diseases 2021 3 -
Molecular epidemiology of Respiratory Syncytial Virus in children in sub-Saharan Africa.
Marlene Ihling Clara et al. Tropical medicine & international health : TM & IH 2021 3
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Genome-Wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits.
Dammann Allison N et al. PLoS pathogens 2021 3 (3) e1009116 -
Differential induction of Shiga toxin in environmental Escherichia coli O145:H28 strains carrying the same genotype as the outbreak strains.
Carter Michelle Qiu et al. International journal of food microbiology 2020 12 109029 -
Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England
Grint DJ, et al. medRxiv, Mar 10, 2021. -
The N501Y spike substitution enhances SARS-CoV-2 transmission
Liu Y, et al. bioRxiv, Mar 9, 2021. -
Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation
Deng X, et al. medRxiv, Mar 9, 2021. -
Viral evolution sustains a dengue outbreak of enhanced severity.
Inizan Catherine et al. Emerging microbes & infections 2021 3 1-27
DETECTION / DIAGNOSIS
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Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs.
Bowden Katherine E et al. mSphere 2021 3 (2)
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SARS-CoV-2 Direct Detection Without RNA Isolation With Loop-Mediated Isothermal Amplification (LAMP) and CRISPR-Cas12.
Garcia-Venzor Alfredo et al. Frontiers in medicine 2021 3 627679 -
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland
Chen C, et al. medRxiv, Mar 9, 2021. -
Early estimates of SARS-CoV-2 B.1.1.7 variant emergence in a university setting
Johnson KE, et al. medRxiv, Mar 9, 2021. -
Rapid increase of SARS-CoV-2 variant B.1.1.7 detected in sewage samples from England between October 2020 and January 2021
Wilton T, et al. medRxiv, Mar 7, 2021.
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Redesigning SARS-CoV-2 clinical RT-qPCR assays for wastewater RT-ddPCR
Gonzalez R, et al. medRxiv, Mar 5, 2021. -
Assessing the feasibility and effectiveness of household-pooled universal testing to control COVID-19 epidemics.
Libin Pieter J K et al. PLoS computational biology 2021 3 (3) e1008688 -
The role of ultra-sensitive molecular methods for detecting malaria - the broader perspective
Kamaliddin C, et al. Clin Infect Dis. 2021 Mar 9;ciab221.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Utility of whole genome sequencing during an investigation of multiple foodborne outbreaks of Shigella sonnei
Mikhail AF, et al. Epidemiol Infect. 2021 Mar 1;1-23. -
SARS-CoV-2 transmission in intercollegiate athletics not fully mitigated with daily antigen testing.
Moreno Gage K et al. medRxiv : the preprint server for health sciences 2021 3
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Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco.
Peng James et al. medRxiv : the preprint server for health sciences 2021 3 -
Validation of molecular clock inferred HIV infection ages: Evidence for accurate estimation of infection dates.
Kostaki Evangelia Georgia et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 3 104799 -
Epidemiological dynamics of enterovirus D68 in the United States and implications for acute flaccid myelitis
Park SW, et al. Sci Transl Med. 2021 Mar 10;13(584):eabd2400.
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes
Saad-Roy CM, et al. Science, Mar 9, 2021. -
A recombinant ACE2 Triple Decoy that traps and neutralizes SARS-CoV-2 shows enhanced affinity for highly transmissible SARS-CoV-2 variants
Tanaka S, et al. bioRxiv, Mar 9, 2021.
HOST-MICROBE INTERACTIONS
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Genome-wide association study of resistance to Mycobacterium tuberculosis infection identifies a locus at 10q26.2 in three distinct populations.
Quistrebert Jocelyn et al. PLoS genetics 2021 3 (3) e1009392 -
A common TMPRSS2 variant protects against severe COVID-19
David A, et al. medRxiv, Mar 8, 2021. -
Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2.
Baggen Jim et al. Nature genetics 2021 3 -
Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies
Muecksch F, et al. bioRxiv, Mar 8, 2021. -
Association between ABO blood types and coronavirus disease 2019 (COVID-19), genetic associations, and underlying molecular mechanisms: a literature review of 23 studies.
Zhang Yujia et al. Annals of hematology 2021 3
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Can ACE2 Receptor Polymorphism Predict Species Susceptibility to SARS-CoV-2?
Devaux Christian A et al. Frontiers in public health 2021 3 608765
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 updated:Jan 9, 2025