Advanced Molecular Detection Clips Content (Published on 05/06/2021)
NEWS
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Reactive, reproducible, collaborative: computational notebooks evolve
Perkel JM. Nature, May 3, 2021. -
Pandemic Pushes Handheld qPCR Devices Closer to Commercialization
Johnson M. GenomeWeb, Apr 30, 2021. -
Scientists set out to connect the dots on long COVID
Marx V. Nat Methods, Apr 28, 2021. -
Sewage Sampling Robots Speed SARS-CoV-2 Detection
Williams R. The Scientist, May 1, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Coronavirus (COVID-19) Testing
(website) Our World in Data, last update April 9, 2021.
CONCEPTS / COMMENTS
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Interplay between Emerging SARS-CoV-2 Variants and Pandemic Control.
Neuzil Kathleen M et al. The New England journal of medicine 2021 5 -
Unlocking capacities of viral genomics for the COVID-19 pandemic response.
Knyazev Sergey et al. ArXiv 2021 5
METHODS / TOOLS
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Species-Specific Quality Control, Assembly and Contamination Detection in Microbial Isolate Sequences with AQUAMIS.
Deneke Carlus et al. Genes 2021 5 (5) -
Detect and destroy: CRISPR-based technologies for the response against viruses.
Freije Catherine A et al. Cell host & microbe 2021 4 -
SARS-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples
Lam C, et al. bioRxiv, May 3, 2021.
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Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring
Maier W, et al. bioRxiv, Mar 25, 2021. -
Sequencing SARS-CoV-2 in a malaria research laboratory in Mali, West Africa: the road to sequencing the first SARS-CoV-2 genome in Mali
Dara A, et al. bioRxiv, May 5, 2021. -
Estimating vaccine efficacy against transmission via effect on viral load
Kennedy-Shaffer L, et al. medRxiv, May 6, 2021. -
A cross-country database of COVID-19 testing.
Hasell Joe et al. Scientific data 2020 10 (1) 345
EVOLUTION / ECOLOGY / POPULATIONS
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New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China
Shi Liyuan et al. Frontiers in microbiology 2021 5 628335 -
Population structure and transmission of Mycobacterium bovis in Ethiopia.
Almaw Gizat et al. Microbial genomics 2021 5 (5) -
Within-host evolution of SARS-CoV-2 in an immunosuppressed COVID-19 patient: a source of immune escape variants
Weigang S, et al. medRxiv, May 5, 2021. -
Preliminary report on SARS-CoV-2 Spike mutation T478K.
Di Giacomo Simone et al. Journal of medical virology 2021 5 -
Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy.
Di Giallonardo Francesca et al. Viruses 2021 5 (5) -
Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada
Sjaarda CP, et al. mSphere. 2021 May 5;6(3):e00011-21. -
Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study.
Capozzi Loredana et al. Viruses 2021 5 (5) -
Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals
Braun K, et al. bioRxiv, Apr 30, 2021. -
Evolutionary analysis of SARS-CoV-2 spike protein for its different clades.
Pereson Matías J et al. Journal of medical virology 2021 1 (5) 3000-3006 -
Temporal Dominance of B.1.1.7 over B.1.354 SARS-CoV-2 Variant: A Hypothesis Based on Areas of Variant Co-Circulation.
Kostaki Evangelia Georgia et al. Life (Basel, Switzerland) 2021 5 (5) -
One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages.
González-Candelas Fernando et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 4 104869 -
Betacoronaviruses genome analysis reveals evolution toward specific codons usage: implications for SARS-CoV-2 mitigation strategies.
Lopes Elisson Nogueira et al. Journal of medical virology 2021 5 -
Temporal and geographic spreading of hepatitis B virus genotype A (HBV-A) in Brazil and the Americas.
Wolf Jonas Michel et al. Journal of viral hepatitis 2021 5 -
The Long-Term Impact of Rotavirus Vaccines in Korea, 2008-2020; Emergence of G8P[8] Strain.
Kim Kwang Gon et al. Vaccines 2021 5 (4)
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Long-term surveillance for hepatitis E virus in an Italian two-site farrow-to-finish swine farm.
Ianiro Giovanni et al. Zoonoses and public health 2021 5 -
Rotavirus Strain Distribution before and after Introducing Rotavirus Vaccine in India.
Varghese Tintu et al. Pathogens (Basel, Switzerland) 2021 5 (4)
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Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012-2019.
Farrag Mohamed A et al. Virology journal 2021 5 (1) 90 -
Adaptive Evolution of New Variants of Dengue Virus Serotype 1 Genotype V Circulating in the Brazilian Amazon.
Ribeiro Geovani de Oliveira et al. Viruses 2021 5 (4) -
Nationwide Distribution of Dengue Virus Type 3 (DENV-3) Genotype I and Emergence of DENV-3 Genotype III during the 2019 Outbreak in Bangladesh.
Titir Snigdha Rahman et al. Tropical medicine and infectious disease 2021 5 (2) -
Intrahost speciations and host switches played an important role in the evolution of herpesviruses.
Brito Anderson F et al. Virus evolution 2021 5 (1) veab025 -
Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years.
Cho Young-Keol et al. Viruses 2021 5 (5)
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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The Bacterial Genomic Context of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases Highlights an Emerging Threat to Public Health.
Lemay-St-Denis Claudèle et al. Antibiotics (Basel, Switzerland) 2021 5 (4) -
Whole-genome characterization of hemolytic uremic syndrome-causing Shiga toxin-producing Escherichia coli in Sweden.
Hua Ying et al. Virulence 2021 5 (1) 1296-1305 -
Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins.
McDougall Fiona K et al. Microbial genomics 2021 5 (5) -
Stepwise pathogenic evolution of Mycobacterium abscessus.
Bryant Josephine M et al. Science (New York, N.Y.) 2021 5 (6541) -
Colonization with multidrug-resistant Enterobacteriaceae among infants: an observational study in southern Sri Lanka.
Meredith Hannah R et al. Antimicrobial resistance and infection control 2021 5 (1) 72 -
Molecular characterization of Neisseria gonorrhoeae isolates collected through a national surveillance programme in Japan, 2013: evidence of the emergence of a ceftriaxone-resistant strain from a ceftriaxone-susceptible lineage.
Hanao Mami et al. The Journal of antimicrobial chemotherapy 2021 5 -
Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005-2009.
Naicker Serisha D et al. Journal of fungi (Basel, Switzerland) 2021 5 (5)
DETECTION / DIAGNOSIS
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Simultaneous detection and differentiation of clinically relevant relapsing fever Borrelia with semi-multiplex real-time PCR.
Dietrich Elizabeth A et al. Journal of clinical microbiology 2021 4
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Comparison of Molecular and In Silico Salmonella Serotyping for Salmonella Surveillance.
Chui Linda et al. Microorganisms 2021 5 (5)
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Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico.
Delgado-Suárez Enrique Jesús et al. PloS one 2021 5 (5) e0243681 -
Implementation of SARS-CoV2 Screening in K-12 Schools using In-School Pooled Molecular Testing and Deconvolution by Rapid Antigen Test
Pollock NR, et al. medRxiv, May 5, 2021.
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COVID-19 monitoring in rural communities: First comparison of lagoon and pumping station samples for wastewater-based epidemiology
D'Aoust DM, et al. medRxiv, May 4, 2021.
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The surveillance of spike protein for patients with COVID-19 detected in Hong Kong in 2020.
Mak Gannon Ck et al. Journal of medical virology 2021 5
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SARS-CoV-2 detection on self-collected saliva or anterior nasal specimens compared with healthcare personnel-collected nasopharyngeal specimens.
Marx Grace E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 4
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Presence of SARS-CoV-2 Nucleoprotein in Cardiac Tissues of Donors with Negative COVID-19 Molecular Tests.
Perrucci Gianluca Lorenzo et al. Diagnostics (Basel, Switzerland) 2021 5 (4) -
Wastewater Surveillance for SARS-CoV-2 on College Campuses: Initial Efforts, Lessons Learned, and Research Needs.
Harris-Lovett Sasha et al. International journal of environmental research and public health 2021 5 (9)
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Genomic Analysis and Lineage Identification of SARS-CoV-2 Strains in Migrants Accessing Europe Through the Libyan Route.
Tramuto Fabio et al. Frontiers in public health 2021 5 632645 -
Testing at scale during the COVID-19 pandemic
Mercer TR, Salit M. Nat Rev Genet, May 4, 2021.
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Retrospective Detection of SARS-CoV-2 in Symptomatic Patients prior to Widespread Diagnostic Testing in Southern California.
Hilt Evann E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 5 -
Identification of and Surveillance for the SARS-CoV-2 Variants B.1.427 and B.1.429--Colorado, January-March 2021
Webb LM, et al. MMWR, May 5, 2021.
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Hepatitis E virus: Whole genome sequencing as a new tool for understanding HEV epidemiology and phenotypes.
Davis Christopher A et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2021 5 104738 -
"Kankasha" in Kassala: A prospective observational cohort study of the clinical characteristics, epidemiology, genetic origin, and chronic impact of the 2018 epidemic of Chikungunya virus infection in Kassala, Sudan.
Bower Hilary et al. PLoS neglected tropical diseases 2021 5 (4) e0009387 -
Blood Virosphere in Febrile Tanzanian Children.
Cordey Samuel et al. Emerging microbes & infections 2021 5 1-237 -
Targeted deep amplicon sequencing of antimalarial resistance markers in Plasmodium falciparum isolates from Cameroon.
L'Episcopia Mariangela et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 5
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses.
Bainomugisa Arnold et al. Microbial genomics 2021 5 (5) -
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.
Müller Nicola F et al. Science translational medicine 2021 5 -
Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant -- New York City, New York, January 1-April 5, 2021
Thompson CN, et al. MMWR, May 5, 2021. -
COVID-19: first long-term care facility outbreak in the Netherlands following cross-border introduction from Germany, March 2020.
van Hensbergen Mitch et al. BMC infectious diseases 2021 5 (1) 418
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Nosocomial Outbreak of SARS-CoV-2 in a "Non-COVID-19" Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission.
Borges Vítor et al. Viruses 2021 5 (4) -
COVID-19 Outbreak Associated with a SARS-CoV-2 R.1 Lineage Variant in a Skilled Nursing Facility After Vaccination Program - Kentucky, March 2021.
Cavanaugh Alyson M et al. MMWR. Morbidity and mortality weekly report 2021 4 (17) 639-643
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A main event and multiple introductions of SARS-CoV-2 initiated the COVID-19 epidemic in Greece.
Spanakis Nikolaos et al. Journal of medical virology 2021 1 (5) 2899-2907 -
Use of whole genome sequencing to investigate a cluster of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in emergency department personnel.
Chan Ernest R et al. Infection control and hospital epidemiology 2021 5 1-10
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Incursions of rabbit hemorrhagic disease virus 2 in Canada - clinical, molecular and epidemiological investigation.
Ambagala Aruna et al. Transboundary and emerging diseases 2021 4 -
Molecular surveillance of HIV-1 newly diagnosed infections in Shenzhen, China from 2011 to 2018.
Zhang Dong et al. The Journal of infection 2021 5
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Neutralization of B.1.1.28 P2 variant with sera of natural SARS-CoV-2 infection and recipients of BBV152 vaccine
Sapkal G, et al. bioRxiv, Apr 30, 2021. -
Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant.
Shinde Vivek et al. The New England journal of medicine 2021 5 -
Influenza viral particles harboring the SARS-CoV-2 spike RBD as a combination respiratory disease vaccine
Chaparian RR, et al. bioRxiv, Apr 30, 2021. -
Microbial Genomics as a Catalyst for Targeted Antivirulence Therapeutics.
Sintchenko Vitali et al. Frontiers in medicine 2021 5 641260
HOST-MICROBE INTERACTIONS
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Prior SARS-CoV-2 infection rescues B and T cell responses to variants after first vaccine dose.
Reynolds Catherine J et al. Science (New York, N.Y.) 2021 5 -
Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes.
Voss William N et al. Science (New York, N.Y.) 2021 5
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HPV infection and bacterial microbiota in the semen from healthy men.
Tuominen Heidi et al. BMC infectious diseases 2021 4 (1) 373 -
Assessment of Mixed Plasmodium falciparum sera5 Infection in Endemic Burkitt Lymphoma: A Case-Control Study in Malawi.
Arisue Nobuko et al. Cancers 2021 5 (7)
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.
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- Page last updated:Sep 21, 2023
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