Advanced Molecular Detection Clips Content (Published on 04/01/2021)
NEWS
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Scientists can now sequence an entire genome overnight. This technology has been the key tool in identifying and tracking Covid variants. Unlocking the Covid Code
Gertner J. New York Times, Mar 25, 2021. -
Genomic surveillance: What it is and why we need more of it to track coronavirus variants and help end the COVID-19 pandemic
Sundermann A, et al. The Conversation, Mar 31, 2021. -
Report on COVID origins highlights clues to animal-human jump
Schnirring L. CIDRAP, Mar 30, 2021. -
WHO report into COVID pandemic origins zeroes in on animal markets, not labs
Maxmen A. Nature, Mar 30, 2021. -
COVID-19 Variants Now Detected in Animals, May Find Hosts in Mice
Goodman B. Medscape, Mar 24, 2021. -
Stanford Scientists Reverse Engineer Moderna Vaccine, Post Code on Github
Gault M. Vice, Mar 29, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Pathogenwatch: A Global Platform for Genomic Surveillance
(website) Centre for Genomic Pathogen Surveillance, accessed Mar 31, 2021. -
SARS-CoV-2 (hCoV-19) Mutation Reports. Lineage | Mutation Tracker
(website) Center for Viral Systems Biology, Scripps Research, accessed Mar 31, 2021. -
SARS-CoV-2 (hCoV-19) Mutation Reports: Lineage Comparison
(website) outbreak.info, accessed Mar 31, 2021.
POLICY
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Origins of the SARS-CoV-2 virus: WHO-convened Global Study of the Origins of SARS-CoV-2
(report) World Health Organization (WHO), March 30, 2021. -
Joint Statement on the WHO-Convened COVID-19 Origins Study
(statement) US Dept of State, Mar 30, 2021. -
EU Statement on the WHO-led COVID-19 origins study
(statement) Delegation of the European Union to the UN and other international organisations in Geneva -
SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests
(guidance) FDA, Mar 30, 2021.
CONCEPTS / COMMENTS
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Perspective: Diagnostic laboratories should urgently develop T cell assays for SARS-CoV-2 infection.
Ameratunga Rohan et al. Expert review of clinical immunology 2021 3
METHODS / TOOLS
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Supervised learning on phylogenetically distributed data.
Layne Elliot et al. Bioinformatics (Oxford, England) 2021 1 (Suppl_2) i895-i902 -
Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli.
Haendiges Julie et al. PloS one 2021 3 (3) e0242294 -
Sieve analysis to understand how SARS-CoV-2 diversity can impact vaccine protection.
Rolland Morgane et al. PLoS pathogens 2021 3 (3) e1009406 -
Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD.
Marcon Yannick et al. PLoS computational biology 2021 3 (3) e1008880
EVOLUTION / ECOLOGY / POPULATIONS
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Epidemiologic and Genomic Reidentification of Yaws, Liberia.
Timothy Joseph W S et al. Emerging infectious diseases 2021 3 (4) 1123-1132 -
Emergence of Burkholderia pseudomallei Sequence Type 562, Northern Australia.
Meumann Ella M et al. Emerging infectious diseases 2021 3 (4) 1057-1067 -
The global dissemination of hospital clones of Enterococcus faecium
van Hal SJ, et al. Genome Med. 2021 Mar 30;13(1):52. -
Single-nucleotide polymorphism-based epidemiological analysis of Korean Mycobacterium bovis isolates
Kim Tae Woon et al. Journal of veterinary science 2021 3 (2) e24 -
Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution.
Chaillon A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 3 -
Preliminary report on SARS-CoV-2 Spike mutation T478K
Di Giacomo S, et al. bioRxiv, Mar 29, 2021. -
Emergence of a SARS-CoV-2 E484K variant of interest in Arizona
Skidmore PT, et al. medRxiv, Mar 28, 2021. -
How unequal vaccine distribution promotes the evolution of vaccine escape
Gerrish P, et al. medRxiv, Mar 28, 2021. -
A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa
de Oliveira T, et al. krisp.org, Mar 25, 2021. -
Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26-February 16, 2021.
Haim-Boukobza Stéphanie et al. Emerging infectious diseases 2021 3 (5) -
Emergence and spread of SARS-CoV-2 lineages B.1.1.7 and P.1 in Italy
Di Giallonardo F, et al. medRxiv, Mar 28, 2021. -
The new SARS-CoV-2 variant and reinfection in the resurgence of COVID-19 outbreaks in Manaus, Brazil
He D, et al. medRxiv, Mar 28, 2021. -
Multiple clades of Husavirus in South America revealed by next generation sequencing.
Ramos Endrya do Socorro Fôro et al. PloS one 2021 3 (3) e0248486 -
Phylogenetic and Mutational Analysis of Lassa Virus Strains Isolated in Nigeria: Proposal for an In Silico Study.
Kolawole Daniel et al. JMIR research protocols 2021 3 (3) e23015 -
An Integrated Molecular Approach to Untangling Host-Vector-Pathogen Interactions in Mosquitoes (Diptera: Culicidae) From Sylvan Communities in Mexico.
Hernández-Triana Luis M et al. Frontiers in veterinary science 2021 3 564791
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries.
Sands Kirsty et al. Nature microbiology 2021 3 (4) 512-523 -
Resistance to Second-Line Anti-TB Drugs in Cambodia: A Phenotypic and Genetic Study.
Cheng Sokleaph et al. Infection and drug resistance 2021 3 1089-1104 -
Phylogenetic context of Shiga toxin-producing Escherichia coli serotype O26:H11 in England
Dallman Timothy J et al. Microbial genomics 2021 3 -
Poultry Ownership and Genetic Antibiotic Resistance Determinants in the Gut of Preschool Children.
Brogdon Jessica M et al. The American journal of tropical medicine and hygiene 2021 3 -
ESBL and E. coli From Pig and Pig Farm Workers in Vietnam and Their Association With Mobile Genetic Elements
Hounmanou Yaovi Mahuton Gildas et al. Frontiers in microbiology 2021 3 629139 -
Colistin-resistant Klebsiella pneumoniae bloodstream infection: old drug, bad bug.
Ben-Chetrit Eli et al. Archives of microbiology 2021 3 -
Insights on the Structural Variations of the Furin-Like Cleavage Site Found Among the December 2019-July 2020 SARS-CoV-2 Spike Glycoprotein: A Computational Study Linking Viral Evolution and Infection.
Cueno Marni E et al. Frontiers in medicine 2021 3 613412 -
Sequence analysis of SARS-CoV-2 in nasopharyngeal samples from patients with COVID-19 illustrates population variation and diverse phenotypes, placing the in vitro growth properties of B.1.1.7 and B.1.351 lineage viruses in context.
Prince T, et al. bioRxiv, Mar 30, 2021. -
Emerging SARS-CoV-2 mutation hotspots associated with clinical outcomes
Pang X, et al. bioRxiv, Mar 31, 2021. -
Surveillance of Influenza A resistance to polymerase complex inhibitors by whole genome analysis, 2016-17, 2017-18 and 2018-19 Seasons, Eastern Spain.
Mengual-Chuliá Beatriz et al. Antimicrobial agents and chemotherapy 2021 3 -
Molecular Characteristics, Antigenicity, Pathogenicity, and Zoonotic Potential of a H3N2 Canine Influenza Virus Currently Circulating in South China.
Wu Meihua et al. Frontiers in microbiology 2021 3 628979 -
Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris.
Muñoz José F et al. Genetics 2021 3 -
Atovaquone/Proguanil Resistance in an Imported Malaria Case in Chile.
Chenet Stella M et al. The American journal of tropical medicine and hygiene 2021 3
DETECTION / DIAGNOSIS
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Twenty-first century molecular methods for analyzing antimicrobial resistance in surface waters to support One Health assessments.
Franklin A M et al. Journal of microbiological methods 2021 3 106174 -
Prevalence and genomic investigation of Salmonella isolates recovered from animal food-chain in Xinjiang, China.
Liu Yingyu et al. Food research international (Ottawa, Ont.) 2021 3 110198 -
High Diversity, Prevalence, and Co-infection Rates of Tick-Borne Pathogens in Ticks and Wildlife Hosts in an Urban Area in Romania.
Borsan Silvia-Diana et al. Frontiers in microbiology 2021 3 645002 -
Next-Generation Sequencing Analysis of Pathogenic Leptospira: A Way Forward for Understanding Infectious Disease Dynamics in Low/Middle-Income, Disease-Endemic Settings.
Agampodi Suneth B et al. The American journal of tropical medicine and hygiene 2021 3 -
Economic evaluation of whole genome sequencing for pathogen identification and surveillance - results of case studies in Europe and the Americas 2016 to 2019.
Frank Alleweldt et al. Euro Surveill 2021 3 (9) -
DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing.
Lagerborg Kim A et al. bioRxiv : the preprint server for biology 2021 3 -
Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing.
Peto Leon et al. Journal of clinical microbiology 2021 3 -
Evaluating recovery, cost, and throughput of different concentration methods for SARS-CoV-2 wastewater-based epidemiology.
LaTurner Zachary W et al. Water research 2021 3 117043 -
Quantitative detection of SARS-CoV-2 B.1.1.7 variant in wastewater by allele-specific RT-qPCR
Lee WL, et al. medRxiv, Mar 29, 2021. -
A Novel Diagnostic Test to Screen SARS-CoV-2 Variants Containing E484K and N501Y Mutations
Zhao Y, et al. medRxiv, Mar 29, 2021. -
A novel single nucleotide polymorphism assay for the detection of N501Y SARS-CoV-2 variants.
Sandoval Torrientes M et al. Journal of virological methods 2021 3 114143 -
Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples
Napit R, et al. medRxiv, Mar 30, 2021. -
Rapid identification and tracking of SARS-CoV-2 variants of concern.
Chakraborty Debojyoti et al. Lancet (London, England) 2021 3 -
Emergence of N antigen SARS-CoV-2 genetic variants escaping detection of antigenic tests
Del Vecchio C, et al. medRxiv, Mar 26, 2021. -
First wastewater surveillance-based city zonation for effective COVID-19 pandemic preparedness powered by early warning: A study of Ahmedabad, India
Kumar M, et al. medRxiv, Mar 20, 2021. -
Rapid Detection of SARS-CoV-2 Variants of Concern, Including B.1.1.28/P.1, in British Columbia, Canada.
Matic Nancy et al. Emerging infectious diseases 2021 3 (6) -
Emerging Non-Polio Enteroviruses recognized in the framework of the Acute Flaccid Paralyses (AFP) surveillance system in Northern Italy, 2016-2018.
Pellegrinelli Laura et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 3 -
Viral shedding in gastroenteritis in children caused by variants and novel recombinant norovirus infections.
Cheng Hung-Yen et al. Medicine 2021 3 (12) e25123 -
Genetic diversity and molecular epidemiological characterization of group A rotaviruses in raw sewage in Jinan by next generation sequencing.
Du Haibo et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 3 104814 -
Lessons from intensified surveillance of viral hepatitis A, Israel, 2017 and 2018.
Gozlan Yael et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 2 (6) -
Suitability of current typing procedures to identify epidemiologically linked human Giardia duodenalis isolates.
Woschke Andreas et al. PLoS neglected tropical diseases 2021 3 (3) e0009277 -
DNA-based detection of Leptospira wolffii, Giardia intestinalis and Toxoplasma gondii in environmental feces of wild animals in Korea.
Kumari Priyanka et al. The Journal of veterinary medical science 2021 3
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients.
León-Sampedro Ricardo et al. Nature microbiology 2021 3 -
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England.
Volz Erik et al. Nature 2021 3 -
Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface
Li KK, et al. medRxiv, Mar 26, 2021. -
Phylogenomic analysis of COVID-19 summer and winter outbreaks in Hong Kong: An observational study.
Chan Wan-Mui et al. The Lancet Regional Health. Western Pacific 2021 3 100130 -
Phylogenomic tracing of asymptomatic transmission in a COVID-19 outbreak.
Zhang Ju et al. Innovation (New York, N.Y.) 2021 3 100099 -
Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalisation rate, February 2021, Rio Grande do Sul, Southern Brazil.
Martins Andreza Francisco et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 3 (12) -
Linked transmission chains of imported SARS-CoV-2 variant B.1.351 across mainland France, January 2021
The SARS-CoV-2 variant with lineage B.1.351 clusters investigation team, Eurosurveillance, Apr 2021. -
Genomic variation and epidemiology of SARS-CoV-2 importation and early circulation in Israel.
Zuckerman Neta S et al. PloS one 2021 3 (3) e0243265 -
Preliminary report of an outbreak of SARS-CoV-2 in mink and mink farmers associated with community spread, Denmark, June to November 2020.
Larsen Helle Daugaard et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 2 (5) -
Reconstructing unseen transmission events to infer dengue dynamics from viral sequences.
Salje Henrik et al. Nature communications 2021 3 (1) 1810 -
High impact of molecular surveillance on hepatitis A outbreak case detection in Sweden: a retrospective study, 2009 to 2018.
Riess Maximilian et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 3 (9) -
EHEC O111:H8 strain and norovirus GII.4 Sydney [P16] causing an outbreak in a daycare center, Brazil, 2019.
Spano Liliana Cruz et al. BMC microbiology 2021 3 (1) 95 -
Severe dengue outbreak associated with DENV-3 in the city of Manado, North Sulawesi, Indonesia.
Tatura Suryadi N N et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 3
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection.
Stamatatos Leonidas et al. Science (New York, N.Y.) 2021 3 -
Initial report of decreased SARS-CoV-2 viral load after inoculation with the BNT162b2 vaccine
Levine-Tiefenbrun M, et al. Nature, Mar 29, 2021. -
COVID-19 vaccine impact on rates of SARS-CoV-2 cases and post vaccination strain sequences among healthcare workers at an urban academic medical center: a prospective cohort study
Bouton TC, et al. medRxiv, Mar 31, 2021.
HOST-MICROBE INTERACTIONS
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Monozygotic twins discordant for severe clinical recurrence of COVID-19 show drastically distinct T cell responses to SARS-Cov-2
Castro MV, et al. medRxiv, Mar 28, 2021. -
Germline Genetic Variants of Viral Entry and Innate Immunity May Influence Susceptibility to SARS-CoV-2 Infection: Toward a Polygenic Risk Score for Risk Stratification.
Grolmusz Vince Kornél et al. Frontiers in immunology 2021 3 653489 -
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma.
Cele Sandile et al. Nature 2021 3 -
Innate immune deficiencies in patients with COVID-19
Peyneau M, et al. medRxiv, Mar 31, 2021. -
SARS-CoV-2 variant B.1.1.7 caused HLA-A2+ CD8+ T cell epitope mutations for impaired cellular immune response
Xiao C, et al. bioRxiv, Mar 29, 2021. -
Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19.
Rodriguez Christophe et al. PLoS pathogens 2021 3 (3) e1009416 -
Transmissibility and Viral Replication of SARS-COV-2 in Immunocompromised Patients.
Beran Azizullah et al. Journal of medical virology 2021 3 -
Endogenous IFN-beta expression predicts outcome in critical patients with COVID-19
Menezes SM, et al. Lancet Microbe, Mar 30, 2021. -
HIV-1 integration sites in CD4+ T-cells during primary, chronic, and late presentation of HIV-1 infection.
Kok Yik Lim et al. JCI insight 2021 3
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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.
- Page last reviewed:Feb 1, 2024
- Page last updated:Sep 5, 2024