Advanced Molecular Detection Clips Content (Published on 11/04/2021)
NEWS
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America's Food Safety System Failed to Stop a Salmonella Epidemic. It's Still Making People Sick.
Yeung B, et al. ProPublica, Oct 29, 2021. -
Achilles' heel of antibiotic resistance
Khare A. Nat Microbiol, Oct 25, 2021. -
Bacterial Species In the Age of Next-Generation Sequencing
Berman H. ASM.org, Oct 19, 2021. -
Prize for SARS-CoV-2 Sequence Sharing
GenomeWeb, Nov 4, 2021. -
Should Booster Shots Be Required? This Covid question played out long ago, in the fight against smallpox in 1872
Fischetti M. Sci Am, Nov 2, 2021. -
COVID-19 vaccine gives 5 times the protection of 'natural immunity,' data show
Wappes J. CIDRAP, Oct 29, 2021. -
What COVID vaccines for young kids could mean for the pandemic
Kozlov M. Nature, Oct 29, 2021. -
Widespread Coronavirus Infection Found in Iowa Deer, New Study Says
Jacobs A. New York Times, Nov 2, 2021. -
The search for people who never get COVID
Mallapaty S. Nature, Oct 29, 2021. -
Should You Try an At-Home Genetic Test for COVID-19?
Erdmann J. Discover, Nov 1, 2021. -
Hope, Concern Surround WHO Green Light of First Malaria Vaccine
Zimmer K. The Scientist, Oct 28, 2021.
POLICY
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HHS Launches New Program to Speed Up COVID-19 OTC Test Regulatory Process
GenomeWeb, Oct 25, 2021.
CONCEPTS / COMMENTS
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Defective viral RNA sensing linked to severe COVID-19
Schoggins J. Science, Oct 29, 2021. -
SARS-CoV-2 viral RNA levels are not 'viral load'.
Michalakis Yannis et al. Trends in microbiology 2021 9 (11) 970-972 -
Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: An IDSA/ASM Consensus Review Document.
Greninger Alexander L et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 11
METHODS / TOOLS
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Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore Sequencing.
Yan Yi et al. Virologica Sinica 2021 4 (5) 901-912 -
Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing.
Van Poelvoorde Laura A E et al. Frontiers in microbiology 2021 11 747458 -
SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels.
Di Pasquale Adriano et al. BMC genomics 2021 10 (1) 782 -
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
Brejová Brona et al. PloS one 2021 10 (10) e0259277 -
Detailed Overview of the Buildout and Integration of an Automated High-Throughput CLIA Laboratory for SARS-CoV-2 Testing on a Large Urban Campus
Landaverde L, et al. medRxiv, Nov 1, 2021. -
Early sample tagging and pooling enables simultaneous SARS-CoV-2 detection and variant sequencing.
Chappleboim Alon et al. Science translational medicine 2021 9 (618) eabj2266 -
A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19.
Zhu Zijun et al. Briefings in bioinformatics 2021 10 -
Optimisation of methodology for whole genome sequencing of Measles Virus directly from patient specimens
Schulz H, et al. J Virol Methods. 2021 Oct 30;114348.
EVOLUTION / ECOLOGY / POPULATIONS
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Gene flow and Bayesian phylogeography of serogroup C meningococci circulating in Italy.
Lo Presti Alessandra et al. Annali dell'Istituto superiore di sanita 2020 12 (4) 430-436 -
Phylogenetic and antimicrobial drug resistance analysis of Vibrio cholerae O1 isolates from Ghana.
Opintan Japheth A et al. Microbial genomics 2021 10 (10) -
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil
Moreira FR, et al. Virus Evol. 2021 Oct 1;7(2):veab087. -
SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India.
Cherian Sarah et al. Microorganisms 2021 8 (7) -
Multiple spillovers and onward transmission of SARS-Cov-2 in free-living and captive White-tailed deer (Odocoileus virginianus)
Kuchipudi SV, et al. bioRxiv, Nov 1, 2021. -
Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics.
Grosche Victória Riquena et al. Microbial genomics 2021 11 (11) -
Genomic surveillance reveals the detection of SARS-CoV-2 Delta, Beta and Gamma VOCs during the third wave in Pakistan.
Umair Massab et al. Journal of medical virology 2021 11 -
Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil.
Moreira Filipe Romero Rebello et al. Virus evolution 2021 11 (2) veab087 -
Molecular Determinants of SARS-CoV-2 Variants.
Banerjee Arinjay et al. Trends in microbiology 2021 8 (10) 871-873 -
Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom's first national lockdown.
Munis Altar M et al. Scientific reports 2021 11 (1) 21484 -
Characterization of HIV-1 Epidemic in Kyrgyzstan.
Sivay Mariya V et al. Frontiers in microbiology 2021 11 753675 -
Factors Influencing Distribution of Coccidioides immitis in Soil, Washington State, 2016.
Nancy A Chow et al. mSphere 2021 11 (6) e0059821 -
Single-genome sequencing reveals within-host evolution of human malaria parasites.
Dia Aliou et al. Cell host & microbe 2021 9 (10) 1496-1506.e3 -
Taxonomy and molecular epidemiology of Cryptosporidium and Giardia - a 50 year perspective (1971-2021).
Ryan Una M et al. International journal for parasitology 2021 10 -
Cryptosporidium hominis Phylogenomic Analysis Reveals Separate Lineages With Continental Segregation.
Cabarcas Felipe et al. Frontiers in genetics 2021 11 740940
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Transmission of Mycobacterium tuberculosis presenting unusually high discordance between genotypic and phenotypic resistance to rifampicin in an endemic tuberculosis setting.
Brandao Angela Pires et al. Tuberculosis (Edinburgh, Scotland) 2020 10 102004 -
Characterization of Drug-Resistant Lipid-Dependent Differentially Detectable Mycobacterium tuberculosis.
Mesman Annelies W et al. Journal of clinical medicine 2021 8 (15) -
Modelling evolutionary pathways for commensalism and hypervirulence in Neisseria meningitidis.
Mullally Christopher A et al. Microbial genomics 2021 10 (10) -
In vitro characterization of six hepatitis B virus genotypes from clinical isolates using transfecting linear HBV genomes.
Zafrullah Mohammad et al. The Journal of general virology 2021 11 (11) -
HIV-1 genetic diversity and natural polymorphisms of the integrase gene in integrase inhibitor naive patients in Harare, Zimbabwe.
Madyadi Amanda et al. AIDS research and human retroviruses 2021 10 -
Prevalence and Molecular Epidemiology of Transmitted Drug Resistance and Genetic Transmission Networks Among Newly Diagnosed People Living With HIV/AIDS in a Minority Area, China.
Yuan Dan et al. Frontiers in public health 2021 10 731280
DETECTION / DIAGNOSIS
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Core Genome Multilocus Sequence Typing and Prediction of Antimicrobial Susceptibility Using Whole-Genome Sequences of Escherichia coli Bloodstream Infection Isolates.
Banerjee Ritu et al. Antimicrobial agents and chemotherapy 2021 8 (11) e0113921 -
Community-level SARS-CoV-2 sequence diversity revealed by wastewater sampling.
Swift Candice L et al. The Science of the total environment 2021 8 149691 -
Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs.
Salido Rodolfo A et al. mSystems 2021 11 e0113621 -
Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13
Arizti-Sanz J, et al. medRxiv, Nov 2, 2021. -
Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction
Ratcliff JD, et al. medRxiv, Nov 2, 2021. -
A review on measurements of SARS-CoV-2 genetic material in air in outdoor and indoor environments: Implication for airborne transmission.
Dinoi Adelaide et al. The Science of the total environment 2021 10 151137 -
Isolation of a Novel Recombinant Canine Coronavirus from a Visitor to Haiti: Further Evidence of Transmission of Coronaviruses of Zoonotic Origin to Humans.
Lednicky John A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 10 -
Genomic surveillance of enterovirus associated with aseptic meningitis cases in southern Spain, 2015-2018.
Gámbaro Fabiana et al. Scientific reports 2021 11 (1) 21523 -
Direct detection of polioviruses using a recombinant poliovirus receptor.
Gerloff Nancy et al. PloS one 2021 11 (11) e0259099
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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A vanA vancomycin-resistant Enterococcus faecium ST80 outbreak resulting from a single importation event.
Pratama Ryanbi et al. The Journal of antimicrobial chemotherapy 2021 10 -
Transmission of multidrug-resistant tuberculosis in Shimen community in Shanghai, China: a molecular epidemiology study.
Han Zhiying et al. BMC infectious diseases 2021 10 (1) 1118 -
A whole-genome sequencing study of an X-family tuberculosis outbreak focus on transmission chain along 25 years.
Comín Jessica et al. Tuberculosis (Edinburgh, Scotland) 2020 12 102022 -
Community transmission and viral load kinetics of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the UK: a prospective, longitudinal, cohort study
Singanayagam A, et al. Lancet Infect Dis, Oct 29, 2021. -
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020.
Muenchhoff Maximilian et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 10 (43) -
Evidence of Early Household Transmission of SARS-CoV-2 Involving a School-aged Child.
Temte Jonathan L et al. WMJ : official publication of the State Medical Society of Wisconsin 2021 10 (3) 233-236 -
Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant.
Elliott Paul et al. Science (New York, N.Y.) 2021 11 eabl9551 -
Surges of hospital-based rhinovirus infection during the 2020 coronavirus disease-19 (COVID-19) pandemic in Beijing, China.
Zhang Ruo-Xi et al. World journal of pediatrics : WJP 2021 10 -
First evidence of human-to-dog transmission of SARS-CoV-2 B.1.160 variant in France.
Medkour Hacène et al. Transboundary and emerging diseases 2021 10 -
Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study
Paredes MI, et al. medRxiv, Oct 27, 2021. -
Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study.
Allen Hester et al. The Lancet regional health. Europe 2021 11 100252 -
Whole genome sequencing confirms Candida albicans and Candida parapsilosis microsatellite sporadic and persistent clones causing outbreaks of candidemia in neonates.
Guinea Jesús et al. Medical mycology 2021 10
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Laboratory-Confirmed COVID-19 Among Adults Hospitalized with COVID-19-Like Illness with Infection-Induced or mRNA Vaccine-Induced SARS-CoV-2 Immunity--Nine States, January-September 2021
Bozio CH, et al. MMWR, Oct 29, 2021. -
BNT162b2 vaccine effectiveness was marginally affected by the SARS-CoV-2 beta variant in fully vaccinated individuals.
Mor Orna et al. Journal of clinical epidemiology 2021 10 -
Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine through 6 Months
Thomas SJ, et al. New Engl J Med, Nov 4, 2021. -
Efficacy of the mRNA-1273 SARS-CoV-2 Vaccine at Completion of Blinded Phase
El Sahly HM, et al. New Engl J Med, Nov 4, 2021. -
BNT162b2 and mRNA-1273 COVID-19 vaccine effectiveness against the SARS-CoV-2 Delta variant in Qatar.
Tang Patrick et al. Nature medicine 2021 11 -
Viral loads of Delta-variant SARS-CoV-2 breakthrough infections after vaccination and booster with BNT162b2.
Levine-Tiefenbrun Matan et al. Nature medicine 2021 11 -
Effectiveness of a third dose of the BNT162b2 mRNA COVID-19 vaccine for preventing severe outcomes in Israel: an observational study
Barda N, et al. Lancet, Oct 29, 2021. -
Risk of Guillain-Barré Syndrome Following Recombinant Zoster Vaccine in Medicare Beneficiaries.
Goud Ravi et al. JAMA internal medicine 2021 11 -
RNA-based therapeutics to treat human fungal infections.
Bruch Alexander et al. Trends in microbiology 2021 10
HOST-MICROBE INTERACTIONS
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Emerging roles of the complement system in host-pathogen interactions.
Sahu Sanjaya K et al. Trends in microbiology 2021 10 -
SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a wide variety of tissues
D'Antonio M, et al. Cell Rep, Nov 2, 2021. -
Associations between Allelic Variants of the Human IgH 3' Regulatory Region 1 and the Immune Response to BNT162b2 mRNA Vaccine.
Colucci Mattia et al. Vaccines 2021 10 (10) -
GWAS loci associated with Chagas cardiomyopathy influences DNA methylation levels.
Casares-Marfil Desiré et al. PLoS neglected tropical diseases 2021 10 (10) e0009874 -
Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis.
Shaw Alexander G et al. BMC microbiology 2021 8 (1) 225
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