Advanced Molecular Detection Clips Content (Published on 05/26/2022)
NEWS
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Health officials in parts of the U.S. see signals in wastewater data hinting at a worsening virus wave.
Paz IG. New York Times, May 20, 2022. -
Another Omicron subvariant, known as BA.2.12.1, has become the dominant form among new U.S. virus cases.
Hassan A. New York Times, May 24, 2022. -
SARS-CoV-2 Genome Analysis Reveals Fitness-Enhancing Mutations
GenomeWeb, May 24, 2022. -
FDA Issues First EUA for Non-Prescription COVID-19/Flu/RSV Test
360dx, May 16, 2022. -
Home testing for syphilis gains support in wake of COVID
Arnold C. Nature, May 19, 2022. -
Viruses that were on hiatus during Covid are back — and behaving in unexpected ways
Branswell H. STAT, May 25, 2022. -
First monkeypox genome from latest outbreak shows links to 2018 strain
LePage M. New Scientist, May 20, 2022. -
Warning signs ahead of monkeypox outbreak went unheeded, experts say
Branswell H. STAT, May 26, 2022. -
Draft Genome Sequence of Latest Monkeypox Virus Unveiled
Putka S. MedPage Today, May 23, 2022. -
Nations eye vaccines for monkeypox, but WHO says mass immunization not urgent
Francis E. Washington Post, May 24, 2022.
EVENTS / TRAINING / WEB RESOURCES
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The New Microbiology: From Microbiomes to CRISPR
(book review) Cossart P. Emerg Infect Dis, Apr 26, 2022. -
Call for Papers: PLOS Medicine Special Issue on Bacterial Antimicrobial Resistance—Surveillance and Prevention
PLoS Medicine, May 17, 2022.
CONCEPTS / COMMENTS
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Antimicrobial resistance data, frugal sequencing, and low-income countries in Africa.
Aruhomukama Dickson et al. The Lancet. Infectious diseases 2022 5 -
A generalizable one health framework for the control of zoonotic diseases.
Ghai Ria R et al. Scientific reports 2022 5 (1) 8588 -
Why do some coronaviruses become pandemic threats when others do not?
Rice Benjamin L et al. PLoS biology 2022 5 (5) e3001652 -
Viral Shedding Kinetics and Transmission of Emerging SARS-CoV-2 Variants-Critical Components of Study Design.
Gowler Camden D et al. JAMA network open 2022 5 (5) e2213614 -
Challenging the Illusion: Health Equity Amidst New Variants.
Essar Mohammad Yasir et al. International journal of public health 2022 5 1604896
METHODS / TOOLS
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Inactivation and Recovery of High Quality RNA From Positive SARS-CoV-2 Rapid Antigen Tests Suitable for Whole Virus Genome Sequencing.
Macori Guerrino et al. Frontiers in public health 2022 5 863862 -
Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking.
Donzelli Sara et al. Computational and structural biotechnology journal 2022 5 -
MutCov: A pipeline for evaluating the effect of mutations in spike protein on infectivity and antigenicity of SARS-CoV-2.
Zhou Wenyang et al. Computers in biology and medicine 2022 4 105509 -
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches.
Thornlow Bryan et al. bioRxiv : the preprint server for biology 2022 5 -
The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology.
Andréoletti Jérémy et al. Systematic biology 2022 5 -
Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example.
Chen Chaoran et al. Epidemics 2022 5 100576
EVOLUTION / ECOLOGY / POPULATIONS
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New Variant of Vibrio parahaemolyticus, Sequence Type 3, Serotype O10:K4, China, 2020
Huang M, et al. Emerg Infect Dis, May 13, 2022. -
Whole-Genome Sequencing of SARS-CoV-2 Reveals Diverse Mutations in Circulating Alpha and Delta Variants during the First, Second and Third Waves of Covid-19 in South Kivu, East of the Democratic Republic of Congo.
Ntagereka Patrick Bisimwa et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2022 5 -
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness.
Obermeyer Fritz et al. Science (New York, N.Y.) 2022 5 abm1208 -
Lebanese SARS-CoV-2 genomics: 24 months of the pandemic.
Fayad Nancy et al. Virus research 2022 5 198824 -
Different evolutionary dynamics of hepatitis B virus genotypes A and D, and hepatitis D virus genotypes 1 and 2 in an endemic area of Yakutia, Russia.
Karlsen Anastasia A et al. BMC infectious diseases 2022 5 (1) 452 -
Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus.
Gaunt Michael W et al. Virus evolution 2022 5 (1) veac027 -
Divergent Rabies Virus Variant of Probable Bat Origin in 2 Gray Foxes, New Mexico, USA
Condori RE, et al. Emerg Infect Dis, May 11, 2022. -
Comparison of herpes simplex virus 1 genomic diversity between adult sexual transmission partners with genital infection.
Rathbun Molly M et al. PLoS pathogens 2022 5 (5) e1010437 -
Ecological divergence of wild birds drives avian influenza spillover and global spread.
Hill Nichola J et al. PLoS pathogens 2022 5 (5) e1010062 -
Retrospective Genomic Characterization of a 2017 Dengue Virus Outbreak, Burkina Faso.
Letizia Andrew G et al. Emerging infectious diseases 2022 5 (6) 1198-1210 -
Off-season RSV epidemics in Australia after easing of COVID-19 restrictions.
Eden John-Sebastian et al. Nature communications 2022 5 (1) 2884 -
Angiostrongylus cantonensis Nematode Invasion Pathway, Mallorca, Spain
Delgado-Serra S, et al. Emerg Infect Dis, May 6, 2022. -
Geographic Population Genetic Structure of the New World Screwworm, Cochliomyia hominivorax (Diptera: Calliphoridae), Using SNPs.
Tietjen Mackenzie et al. Journal of medical entomology 2022 3 (3) 874-882 -
Genetic diversity and population structure of Leishmania (Viannia) braziliensis in the Peruvian jungle.
De Los Santos Maxy B et al. PLoS neglected tropical diseases 2022 5 (5) e0010374
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Diversity of carbapenemase-producing Enterobacterales in England as revealed by whole-genome sequencing of isolates referred to a national reference laboratory over a 30-month period.
Hopkins Katie L et al. Journal of medical microbiology 2022 5 (5) -
A prospective matched case-control study on the genomic epidemiology of colistin-resistant Enterobacterales from Dutch patients.
Vendrik Karuna E W et al. Communications medicine 2022 5 55 -
Variant-specific symptoms of COVID-19 among 1,542,510 people in England
Whitaker M, et al. medRxiv, May 23, 2022. -
Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA.
Bartas Martin et al. Briefings in bioinformatics 2022 3 (3) -
Acquired HIV drug resistance among adults living with HIV receiving first-line antiretroviral therapy in Rwanda: A cross-sectional nationally representative survey.
Musengimana Gentille et al. Antiviral therapy 2022 5 (3) 13596535221102690 -
Clinical epidemiology and high genetic diversity amongst Cryptococcus spp. isolates infecting people living with HIV in Kinshasa, Democratic Republic of Congo.
Bive Bive Zono et al. PloS one 2022 5 (5) e0267842 -
High DDT resistance without apparent association to kdr and Glutathione-S-transferase (GST) gene mutations in Aedes aegypti population at hotel compounds in Zanzibar.
Kampango Ayubo et al. PLoS neglected tropical diseases 2022 5 (5) e0010355
DETECTION / DIAGNOSIS
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Chlamydia trachomatis Variants Escaping Detection in the Aptima Combo 2 Assay in the United States.
Katz Samantha S et al. Sexually transmitted diseases 2022 2 (6) 448-452 -
Low testing rates limit the ability of genomic surveillance programs to monitor SARS-CoV-2 variants: a mathematical modelling study
Han AX, et al. medRxiv, May 23, 2022. -
Dynamic Prediction of Non-Neutral SARS-Cov-2 Variants Using Incremental Machine Learning.
Nicora Giovanna et al. Studies in health technology and informatics 2022 5 654-658 -
SARS-CoV-2 genomic surveillance as an evidence-based infection control approach in an offshore petroleum employee population.
Lamers Susanna L et al. American journal of infection control 2022 5 -
SARS-CoV-2 delta variant infection in domestic dogs and cats, Thailand.
Jairak Waleemas et al. Scientific reports 2022 5 (1) 8403 -
SARS-CoV-2 variant trends in Ireland: Wastewater based epidemiology and clinical surveillance.
Reynolds Liam J et al. The Science of the total environment 2022 5 155828 -
Sequence Proven Reinfections with SARS-CoV-2 at a Large Academic Center
Morris CP, et al. medRxiv, May 19, 2022. -
Identification of Human Case of Avian Influenza A(H5N1) Infection, India
Potdar V, et al. Emerg Infect Dis, May 13, 2022. -
Identifying Japanese Encephalitis Virus Using Metatranscriptomic Sequencing, Xinjiang, China
Yan Y, et al. Emerg Infect Dis, May 13, 2022.
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Zoonotic Transmission of Diphtheria from Domestic Animal Reservoir, Spain
Hoefer A, et al. Emerg Infect Dis, Jun 2022. -
Public Health Response to Multistate Salmonella Typhimurium Outbreak Associated with Prepackaged Chicken Salad, United States, 2018
Greening B, et al. Emerg Infect Dis, Jun 2022. -
Staphylococcus aureus injection drug use-associated bloodstream infections are propagated by community outbreaks of diverse lineages.
Marks Laura R et al. Communications medicine 2022 5 52 -
Rapid Multilateral and Integrated Public Health Response to a Cross-City Outbreak of Salmonella Enteritidis Infections Combining Analytical, Molecular, and Genomic Epidemiological Analysis.
Jiang Min et al. Frontiers in microbiology 2022 5 772489 -
Genomic surveillance uncovers ongoing transmission of carbapenem-resistant Acinetobacter baumannii (CRAB) and identifies actionable routes of transmissions in an endemic setting.
Ong Sean Wei Xiang et al. Infection control and hospital epidemiology 2022 5 1-7 -
Meticillin-susceptible Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing.
Kinnevey P M et al. The Journal of hospital infection 2022 5 -
SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal.
Borges Vítor et al. Communications medicine 2022 5 10 -
A SARS-CoV-2 outbreak associated with vaccine breakthrough in an acute care hospital.
Park Se Yoon et al. American journal of infection control 2022 5 -
First importations of SARS-CoV-2 P.1 and P.2 variants from Brazil to Spain and early community transmission.
Sola Campoy Pedro J et al. Enfermedades infecciosas y microbiologia clinica (English ed.) 2022 5 (5) 262-265
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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Can pulmonary RNA delivery improve our pandemic preparedness?
Merkel Olivia M et al. Journal of controlled release : official journal of the Controlled Release Society 2022 3 549-556 -
COVID-19 vaccine effectiveness against the omicron (BA.2) variant in England
Kirsebom FC, et al. Lancet Infect Dis, May 24, 2022. -
A 2-month field cohort study of SARS-CoV-2 in saliva of BNT162b2 vaccinated nursing home workers.
Saegerman Claude et al. Communications medicine 2022 5 1
HOST-MICROBE INTERACTIONS
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Pandemic, Epidemic, Endemic: B Cell Repertoire Analysis Reveals Unique Anti-Viral Responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus.
Stewart Alexander et al. Frontiers in immunology 2022 5 807104 -
Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection.
Gittelman Rachel M et al. JCI insight 2022 4 (10) -
Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses.
McNaughton Anna L et al. JCI insight 2022 5 -
Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19.
Dannebaum Richard et al. EClinicalMedicine 2022 5 101438 -
The Current Landscape of mRNA Vaccines Against Viruses and Cancer-A Mini Review.
Ladak Reese Jalal et al. Frontiers in immunology 2022 5 885371 -
Gut microbiota predicts body fat change following a low-energy diet: a PREVIEW intervention study.
Jian Ching et al. Genome medicine 2022 5 (1) 54
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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.
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