Advanced Molecular Detection Clips Content (Published on 01/28/2021)
NEWS
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SARS-CoV-2 Test Pooling Hampered by High Positive Rates, Logistical Hurdles
Bonislawski A. 360dx, Jan 21, 2021. -
Denmark is sequencing all coronavirus samples and has an alarming view of the U.K. variant
Birnbaum M, Sorensen MS. Washington Post, Jan 22, 2021. -
Fast-spreading COVID variant can elude immune responses
Callaway E. Nature, Jan 21, 2021. -
UK chief scientist says new virus variant may be more deadly
Lawless J. AP, Jan 22, 2021. -
A Covid-19 peak? Variants muddy forecasts for coming months
Chow D. NBC News, Jan 22, 2021. -
First U.S. case of highly transmissible Brazil coronavirus variant identified in Minnesota
Achenbach J. Washington Post, Jan 25, 2021. -
Coronavirus variant first seen in South Africa identified in South Carolina
Achenbach J, Johnson CY. Washington Post, Jan 28, 2021. -
Why Scientists Are Very Worried About The Variant From Brazil
Doucleff M. NPR, Jan 27, 2021. -
Could a homegrown coronavirus strain be partly to blame for California's surge?
Healy M, Lin II RG. Los Angeles Times, Jan 23, 2021. -
Those Covid-19 variants? ?Don?t worry yet,? vaccine expert says
Herper M. STAT, Jan 27, 2021. -
Covid-19: Moderna plans booster doses to counter variants
Tanne JH. BMJ 2021;372:n232 -
Novavax says its Covid-19 vaccine is 90% effective, but far less so against one variant
Herper M, Garde D. STAT, Jan 28, 2021. -
Amid One Pandemic, Students Train for the Next
Wu KJ. New York Times, Jan 21, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Next Generation Sequencing to Diagnose Primary Immunodeficiency
(blog post) Kantipuly A, Green RF. Office of Genomics and Precision Health, CDC. Jan 22, 2021.
POLICY
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Investigation of novel SARS-CoV-2 variant: Variant of Concern 202012/01
(Technical briefing document) Public Health England, UK. Updated Jan 15, 2021. -
An action plan for pan-European defence against new SARS-CoV-2 variants
Priesemann V, et al. Lancet, Jan 21, 2021.
CONCEPTS / COMMENTS
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The Applications of Nanopore Sequencing Technology in Pathogenic Microorganism Detection
Zhu X, et al. Can J Infect Dis Med Microbiol 2020 Dec 31;2020:6675206. -
COVID-19 Surveillance Data: A Primer for Epidemiology and Data Science.
Tarantola Daniel et al. American journal of public health 2021 Jan e1-e6 -
How epidemiology has shaped the COVID pandemic
(editorial) Nature. 2021 Jan;589(7843):491-492. -
Insights from SARS-CoV-2 sequences
Martin MA, et al. Science, Jan 29, 2021. -
New mutations raise specter of "immune escape"
Kupferschmidt K. Science, Jan 22, 2021.
METHODS / TOOLS
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SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data.
Davis Eric M et al. Genome biology 2021 Jan (1) 37 -
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
Valiente-Mullor Carlos et al. PLoS computational biology 2021 Jan (1) e1008678
EVOLUTION / ECOLOGY / POPULATIONS
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Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution.
Dienstbier Ana et al. Emerging infectious diseases 2021 Jan (1) 57-68 -
Genomic Diversity of Burkholderia pseudomallei Isolates, Colombia
Duarte C, et al. Emerg Infect Dis, Feb 2021. -
Evolution, distribution and genetics of atypical Vibrio cholerae - A review.
Bhandari Murari et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 Jan 104726 -
Characteristics of Salmonella recovered from stools of children enrolled in the Global Enteric Multicenter Study.
Kasumba Irene N et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 Jan -
A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay.
Panzera Y et al. Transboundary and emerging diseases 2021 Jan -
SARS-CoV-2 variants evolved during the early stage of the pandemic and effects of mutations on adaptation in Wuhan populations.
Awadasseid Annoor et al. International journal of biological sciences 2021 (1) 97-106 -
Possible host-adaptation of SARS-CoV-2 due to improved ACE2 receptor binding in mink.
Welkers Matthijs R A et al. Virus evolution 2021 Jan (1) veaa094 -
Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections.
Icer Baykal Pelin B et al. Virus evolution 2021 1 (1) veaa103 -
Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil.
Xavier Joilson et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 Jan
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Spread of Multidrug-Resistant Rhodococcus equi, United States
Alvarez-Narvaez S, et al. Emerg Infect Dis, Feb 21, 2021. -
Unraveling antimicrobial resistance in Helicobacter pylori: Global resistome meets global phylogeny
Domanovich-Asor T, et al. Helicobacter 2021 Jan 25;e12782. -
Compatibility of evolutionary responses to constituent antibiotics drive resistance evolution to drug pairs.
Jahn Leonie Johanna et al. Molecular biology and evolution 2021 Jan -
Antibiotic Treatment Regimes as a Driver of the Global Population Dynamics of a Major Gonorrhea Lineage.
Osnes Magnus N et al. Molecular biology and evolution 2020 Nov -
Genomic Drivers of Multidrug-Resistant Shigella Affecting Vulnerable Patient Populations in the United States and Abroad.
Worley Jay Noboru et al. mBio 2021 Jan (1) -
Evidence of SARS-CoV-2 Replication and Tropism in the Lungs, Airways and Vascular Endothelium of Patients with Fatal COVID-19: An Autopsy Case-Series.
Bhatnagar Julu et al. The Journal of infectious diseases 2021 Jan -
Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020.
Leung Kathy et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 01 (1)
DETECTION / DIAGNOSIS
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cgMLST@Taiwan: A web service platform for Vibrio cholerae cgMLST profiling and global strain tracking.
Chen Yi-Syong et al. Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi 2021 Jan -
Performance of the BinaxNOW coronavirus disease 2019 (COVID-19) Antigen Card test relative to the severe acute respiratory coronavirus virus 2 (SARS-CoV-2) real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay among symptomatic and asymptomatic healthcare employees.
Allison E James et al. Infect Control Hosp Epidemiol 2021 1 (1) 99-101 -
Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants.
Crits-Christoph Alexander et al. mBio 2021 01 (1) -
Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus
Ehrenberg AJ, et al. medRxiv, Jan 26, 2021. -
High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants
Fontenele RS, et al. medRxiv, Jan 25, 2021. -
Bioaerosol sampling for SARS-CoV-2 in a referral center with critically ill COVID-19 patients March-May 2020
Lane MA, et al. Clin Infect Dis. 2021 Jan 28;ciaa1880. -
The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing.
Hanson Kimberly E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 Jan -
Saliva Viral Load Better Correlates with Clinical and Immunological Profiles in Children with Coronavirus Disease 2019.
Chua Gilbert T et al. Emerging microbes & infections 2021 Jan 1-25 -
Early detection of SARS-CoV-2 infection cases or outbreaks at nursing homes by targeted wastewater tracking
Davo L, et al. medRxiv, Jan 22, 2021. -
Strand-Specific Reverse Transcription PCR for Detection of Replicating SARS-CoV-2
Hogan CA, et al. Emerg Infect Dis, Feb 2021. -
Development and Evaluation of Reverse Transcription Loop-Mediated Isothermal Amplification for Rapid and Real-Time Detection of Kyasanur Forest Disease Virus.
Kumar Jyoti S et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 Jan -
Genomic Epidemiology and Active Surveillance to Investigate Outbreaks of Hantaviruses
Kim WK, et al. Front Cell Infect Microbiol 2021 Jan 8;10:532388. -
A new genetic approach to distinguish strains of Anaplasma phagocytophilum that appear not to cause human disease.
Liveris Dionysios et al. Ticks and tick-borne diseases 2021 Jan (3) 101659 -
Evaluation of a Real-Time Recombinase Polymerase Amplification Assay for Rapid Detection of Schistosoma haematobium Infection in Resource-limited Setting.
Frimpong Michael et al. Acta tropica 2021 Jan 105847
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Early Transmission Dynamics, Spread, and Genomic Characterization of SARS-CoV-2 in Panama
Franco D, et al. Emerg Infect Dis, Feb 2021. -
Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy.
Alteri Claudia et al. Nature communications 2021 01 (1) 434 -
Local Transmission of SARS-CoV-2 Lineage B.1.1.7, Brazil, December 2020
Claro IM, et al. Emerg Infect Dis, Mar 2021. -
Epidemiologic Linkage of COVID-19 Outbreaks at Two University-affiliated Hospitals in the Seoul Metropolitan Area in March 2020.
Park Kuenyoul et al. Journal of Korean medical science 2021 Jan (4) e38 -
Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013-2020.
Fabeni Lavinia et al. Viruses 2021 Jan (2) -
Hepatitis C Virus Transmission Clusters in Public Health and Correctional Settings, Wisconsin, USA, 2016-2017
Hochstatter KR, et al. Emerg Infect Dis, Feb 2021. -
Vaccine-Derived Polioviruses, Central African Republic, 2019
Joffret ML, et al. Emerg Infect Dis, Feb 2021. -
First Reported Outbreak of the Emerging Pathogen Candida auris in Canada.
Eckbo Eric J et al. American journal of infection control 2021 Jan -
Genetic Evaluation of Nosocomial Candida auris Transmission.
Roberts Scott C et al. Journal of clinical microbiology 2021 Jan
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization
Wang P, et al. bioRxiv, Jan 26, 2021. -
Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody.
Rappazzo C Garrett et al. Science (New York, N.Y.) 2021 Jan -
Neutralization of spike 69/70 deletion, E484K, and N501Y SARS-CoV-2 by BNT162b2 vaccine-elicited sera
Xie X, et al. bioRxiv, Jan 27, 2021.
HOST-MICROBE INTERACTIONS
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alpha 1-Antitrypsin deficiency and the risk of COVID-19: an urgent call to action
Yang C, et al. Lancet Resp Med, Jan 21, 2021. -
Global absence and targeting of protective immune states in severe COVID-19.
Combes Alexis J et al. Nature 2021 Jan -
Deletion of the NKG2C receptor encoding KLRC2 gene and HLA-E variants are risk factors for severe COVID-19.
Vietzen Hannes et al. Genetics in medicine : official journal of the American College of Medical Genetics 2021 Jan -
Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization
Liu Z, et al. Cell Host Microbe, Jan 27, 2021. -
Prospective mapping of viral mutations that escape antibodies used to treat COVID-19.
Starr Tyler N et al. Science (New York, N.Y.) 2021 Jan -
Human Diversity of Killer Cell Immunoglobulin-Like Receptors and Human Leukocyte Antigen Class I Alleles and Ebola Virus Disease Outcomes.
Wawina-Bokalanga Tony et al. Emerging infectious diseases 2021 Jan (1) 76-84 -
Plasma MicroRNA Profiling of Plasmodium falciparum Biomass and Association with Severity of Malaria Disease
Gupta H, et al. Emerg Infect Dis, Feb 2021. -
Gut microbiome dysbiosis and correlation with blood biomarkers in active-tuberculosis in endemic setting.
Khaliq Aasia et al. PloS one 2021 (1) e0245534
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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