Publication Date: Jun 25, 2020
Advanced Molecular Detection Clips Content
NEWS
- Coronavirus: no evidence new Beijing outbreak came from Europe, EU disease agency says
Elmer K. South China Morning Post, Jun 18, 2020. - Italy sewage study suggests COVID-19 was there in December 2019
Kelland K. Reuters, Jun 19, 2020. - Improved Pool Testing Methods Could Enable COVID-19 Screening as Pandemic Continues
Petrone J. GenomeWeb, June 19, 2020. - Chinese study: Antibodies in COVID-19 patients fade quickly
Roos R. CIDRAP, June 19, 2020. - Decades-Old Soviet Studies Hint at Coronavirus Strategy
Kramer AE. New York Times, Jun 24, 2020. - Here's how genes from Covid-19 survivors could help you--Gene therapy could put an end to future pandemics.
Regalado A. MIT Tech Review, Jun 18, 2020. - Covid-19 Is Bad. But It May Not Be the "Big One"
McKenna M. Wired, Jun 17, 2020.
POLICY
- Research in global health emergencies
Wright K, Harvey K. Nuffield Council on Bioethics, Jan 28, 2020. - A Framework for Managing the COVID-19 Infodemic: Methods and Results of an Online, Crowdsourced WHO Technical Consultation.
Tangcharoensathien Viroj et al. Journal of medical Internet research 2020 Jun - Assessing Solid Organ Donors and Monitoring Transplant Recipients for Human Immunodeficiency Virus, Hepatitis B Virus, and Hepatitis C Virus Infection -- U.S. Public Health Service Guideline, 2020
Jones JM, et al. MMWR, Jun 26, 2020.
CONCEPTS / COMMENTS
- Dating the emergence of human pathogens
Ho SY, Duchene S. Science, Jun 19, 2020. - Could a blood "observatory" stop pandemics?
Bazell R. Science, Jun 26, 2020. - ImmGen at 15.
et al. Nature immunology 2020 Jul (7) 700-703
METHODS / TOOLS
- Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores.
Schwengers Oliver et al. Microbial genomics 2020 Jun - Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping.
Credle Joel J et al. bioRxiv : the preprint server for biology 2020 Jun - Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing.
Noguera-Julian Marc et al. Viruses 2020 Jun (6) - Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes.
Hu Yu et al. iScience 2020 Jun (6) 101223 - The effect of variant interference on de novo assembly for viral deep sequencing.
Castro Christina J et al. BMC genomics 2020 Jun (1) 421 - Blueprint for a pop-up SARS-CoV-2 testing lab.
et al. Nature biotechnology 2020 Jun - Dynamic linkage of COVID-19 test results between Public Health England's Second Generation Surveillance System and UK Biobank.
Armstrong Jacob et al. Microbial genomics 2020 Jun - Evaluation of methods for detecting human reads in microbial sequencing datasets.
Bush Stephen J et al. Microbial genomics 2020 Jun - Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.
Knyazev Sergey et al. Briefings in bioinformatics 2020 Jun - Rapid establishment of a COVID-19 biobank in NHRI by National Biobank Consortium of Taiwan.
Huang Shiu-Feng et al. Biomedical journal 2020 May - Prototyping a Tool for Processing Genetic Meta-Data in Microbiological Laboratories.
Aeschimann Jan et al. Studies in health technology and informatics 2020 Jun 397-401
EVOLUTION / ECOLOGY / POPULATIONS
- Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients.
Constantinides Bede et al. Microbial genomics 2020 Jun - Bacterial communities associated with cell phones and shoes.
Coil David A et al. PeerJ 2020 e9235 - Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species.
Li Chun et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2020 08 104285 - Polymorphism and selection pressure of SARS-CoV-2 vaccine and diagnostic antigens: implications for immune evasion and serologic diagnostic performance
Dumonteil E, Herrera C. bioRxiv, Jun 18, 2020. - Distinct genetic spectrums and evolution patterns of SARS-CoV-2
Liu S, et al. medRxiv, Jun 19, 2020. - Etiology and genetic evolution of canine coronavirus circulating in five provinces of China, during 2018-2019.
He Hai-Jian et al. Microbial pathogenesis 2020 Aug 104209 - Phyloevolutionary analysis of SARS-CoV-2 in Nigeria.
Awoyelu E H et al. New microbes and new infections 2020 Jul 100717 - Spread dynamics of SARS-CoV-2 epidemic in China: a phylogenetic analysis
Guohu H, et al. medRxiv, Jun 20, 2020. - High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States
McNamara RP, et al. bioRxiv, Jun 19, 2020. - Persistence of Severe Acute Respiratory Syndrome Coronavirus 2 in Aerosol Suspensions.
Fears Alyssa C et al. Emerging infectious diseases 2020 Jun (9) - Measles virus and rinderpest virus divergence dated to the sixth century BCE.
Düx Ariane et al. Science (New York, N.Y.) 2020 06 (6497) 1367-1370 - Monitoring of alien mosquitoes in Western Austria (Tyrol, Austria, 2018).
Fuehrer Hans-Peter et al. PLoS neglected tropical diseases 2020 Jun (6) e0008433
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
- Increase of emm1 isolates among group A Streptococcus strains causing scarlet fever in Shanghai, China.
Chen Mingliang et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2020 Jun - Clinical and genomic epidemiology of carbapenem-non-susceptible Citrobacter spp. at a tertiary healthcare center over two decades.
Babiker Ahmed et al. Journal of clinical microbiology 2020 Jun - Whole-genome sequencing analysis of multidrug-resistant Mycobacterium tuberculosis from Java, Indonesia.
Tania Tryna et al. Journal of medical microbiology 2020 Jun - A Unique Clade of SARS-CoV-2 Viruses is Associated with Lower Viral Loads in Patient Upper Airways
Lorenzo-Redondo R, et al. medRxiv, Jun 21, 2020. - Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2.
Banerjee Arinjay et al. Emerging infectious diseases 2020 Jun (9) - Tracing temporal and geographic distribution of resistance to pyrethroids in the arboviral vector Aedes albopictus.
Tancredi Alessandra et al. PLoS neglected tropical diseases 2020 Jun (6) e0008350
DETECTION / DIAGNOSIS
- Evidence Review for Centers for Disease Control and Prevention Guidance Development on Laboratory Testing to Detect Treponema pallidum Infection (Syphilis).
Kersh Ellen N et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jun (Supplement_1) S1-S3 - Molecular and Direct Detection Tests for Treponema pallidum Subspecies pallidum: A Review of the Literature, 1964-2017.
Theel Elitza S et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jun (Supplement_1) S4-S12 - Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses.
Wang Ming et al. Small (Weinheim an der Bergstrasse, Germany) 2020 Jun e2002169 - Performance Assessment of SARS-CoV-2 PCR Assays Developed by WHO Referral Laboratories.
Etievant Sibyle et al. Journal of clinical medicine 2020 Jun (6) - Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2.
Lau Yee Ling et al. PeerJ 2020 e9278 - First environmental surveillance for the presence of SARS-CoV-2 RNA in wastewater and river water in Japan
Haramoto E, medRxiv, Jun 18, 2020. - Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR.
Park Myungsun et al. Experimental & molecular medicine 2020 Jun - Combined point of care nucleic acid and antibody testing for SARS-CoV-2: a prospective cohort study in suspected moderate to severe COVID-19 disease.
Micochova P, et al. medRxiv, Jun 18, 2020. - Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19.
Hanson Kimberly E et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jun - Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India
Arora S, et al. medRxiv, Jun 20, 2020. - Overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for COVID-19 detection.
Esbin Meagan N et al. RNA (New York, N.Y.) 2020 07 (7) 771-783 - Picornavirus etiology of acute infections among hospitalized infants.
Abedi Glen R et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2019 07 39-43 - Emergence of Undetectable Malaria Parasites: A Threat under the Radar amid the COVID-19 Pandemic?
Beshir Khalid B et al. The American journal of tropical medicine and hygiene 2020 Jun - A genotypical study in Benin comparing the carriage of P. falciparum infections before pregnancy and in the early pregnancy: story of a persistent infection.
Jafari-Guemouri Sayeh et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2020 Jun - Barcoded microbial system for high-resolution object provenance.
Qian Jason et al. Science (New York, N.Y.) 2020 06 (6495) 1135-1140
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
- Large Nationwide Outbreak of Invasive Listeriosis Associated with Blood Sausage, Germany, 2018-2019.
Halbedel Sven et al. Emerging infectious diseases 2020 Jul (7) 1456-1464 - Linking Epidemiology and Whole-Genome Sequencing to Investigate Salmonella Outbreak, Massachusetts, USA, 2018.
Vaughn Eric L et al. Emerging infectious diseases 2020 Jul (7) 1538-1541 - Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital.
Neumann Bernd et al. PloS one 2020 (6) e0235160 - Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland.
Crispell Joseph et al. Microbial genomics 2020 Jun - Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.
Walker Andreas et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2020 Jun (22) - Earlier treatment initiation is associated with a decreased number of HIV-1 subtype A1 transmissions in Greece.
Kostaki Evangelia Georgia et al. Sexually transmitted infections 2020 Jun - Notes from the Field: Measles Outbreak Associated with International Air Travel -- California, March-April 2017
Lu L, et al. MMWR, Jun 26, 2020. - Large transmission cluster of acute hepatitis C identified among HIV-positive men who have sex with men in Bangkok, Thailand.
Han Win Min et al. Liver international : official journal of the International Association for the Study of the Liver 2020 Jun
ANTIMICROBIALS / VACCINES / INTERVENTIONS
- Amplifying RNA Vaccine Development.
Fuller Deborah H et al. The New England journal of medicine 2020 06 (25) 2469-2471 - Optimising treatments for sexually transmitted infections: surveillance, pharmacokinetics and pharmacodynamics, therapeutic strategies, and molecular resistance prediction.
Seña Arlene C et al. The Lancet. Infectious diseases 2020 Jun - Landscape and Selection of Vaccine Epitopes in SARS-CoV-2.
Smith Christof C et al. bioRxiv : the preprint server for biology 2020 Jun
HOST-MICROBE INTERACTIONS
- Proteomics Uncovers Immunosuppression in COVID-19 Patients with Long Disease Course
Tang S, et al. medRxiv, Jun 17, 2020. - Host range of SARS-CoV-2 and implications for public health
Santini JM, Edwards SJ. Lancet Microbe, Jun 18, 2020. - Cardiometabolic traits, sepsis and severe covid-19 with respiratory failure: a Mendelian randomization investigation
Ponsford JM, et al. medRxiv, Jun 20, 2020. - Toll Like Receptor 2 promoter -196 to -174 deletion affects CD4 levels along HIV infection progression.
Laplana M et al. The Journal of infectious diseases 2020 Jun
Note:
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 Public Health Genomics 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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