Advanced Molecular Detection Clips Content (Published on 10/07/2021)
NEWS
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Ohio launches variant dashboard to track COVID-19 cases; data shows Delta lessening in state
WHIO, Oct 2, 2021. -
Is the Coronavirus Getting Better at Airborne Transmission?
Mandavilli A. New York Times, Oct 1, 2021. -
Merck's antiviral pill reduces hospitalization of Covid patients, a possible game-changer for treatment
Herper M. STAT, Oct 1, 2021. -
Molnupiravir: coding for catastrophe
Malone B, Campbell EA. Nature Structural & Molecular Biology, 2021. -
COVID vaccines cut the risk of transmitting Delta--but not for long
Mallapaty S. Nature, Oct 5, 2021. -
In major decision, WHO recommends broad rollout of world's first malaria vaccine
Branswell H. STAT, Oct 6, 2021.
EVENTS / TRAINING / WEB RESOURCES
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Bioinformatics mentorship in a resource limited setting.
Jjingo Daudi et al. Briefings in bioinformatics 2021 10
CONCEPTS / COMMENTS
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Progress and challenges in virus genomic epidemiology
Hill V, et al. Trends Parasitol, Oct 4, 2021. -
A Public Health Research Agenda for Managing Infodemics: Methods and Results of the First WHO Infodemiology Conference.
Calleja Neville et al. JMIR infodemiology 2021 10 (1) e30979
METHODS / TOOLS
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Trycycler: consensus long-read assemblies for bacterial genomes.
Wick Ryan R et al. Genome biology 2021 9 (1) 266 -
Mini-XT, a miniaturized tagmentation-based protocol for efficient sequencing of SARS-CoV-2
Fuchs M, et al. medRxiv, Oct 1, 2021. -
ViralFlow: an automated workflow for SARS-CoV-2 genome assembly, lineage assignment, mutations and intrahost variants detection
Dezordi FZ, et al. medRxiv, Oct 1, 2021. -
Classifying COVID-19 Spike Sequences from Geographic Location Using Deep Learning
Ali S, et al. arXiv, Oct 2, 2021. -
A mixture model for determining SARS-Cov-2 variant composition in pooled samples
Valieris R, et al. arXiv, Oct 3, 2021. -
Advances, challenges and opportunities of phylogenetic and social network analysis using COVID-19 data.
Wang Yue et al. Briefings in bioinformatics 2021 10 -
Drug resistance mutations in HIV: new bioinformatics approaches and challenges.
Blassel Luc et al. Current opinion in virology 2021 10 56-64
EVOLUTION / ECOLOGY / POPULATIONS
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Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil.
Almeida Samanta C G et al. Microbial genomics 2021 10 (10) -
Full vaccination against COVID-19 suppresses SARS-CoV-2 delta variant and spike gene mutation frequencies and generates purifying selection pressure
Yeh TY, Contreras. medRxiv, Oct 4, 2021. -
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic.
Jackson Ben et al. Cell 2021 9 (20) 5179-5188.e8 -
Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka.
Jeewandara Chandima et al. Frontiers in microbiology 2021 10 722838 -
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Dudas G, et al. Nat Commun, Oct 1, 2021. -
Genomic diversity of SARS-CoV-2 in Pakistan during fourth wave of pandemic
Umair M, et al. medRxiv, Oct 3, 2021. -
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions.
Dudas Gytis et al. Nature communications 2021 10 (1) 5769 -
Surveillance genome sequencing reveal multiple SARS-CoV-2 variants circulating in the central Texas, USA with a predominance of Delta variant and review of vaccine breakthrough cases.
Mutnal Manohar B et al. Journal of medical virology 2021 10 -
Expansion of a SARS-CoV-2 Delta variant with an 872 nt deletion encompassing ORF7a, ORF7b and ORF8, Poland, July to August 2021.
Mazur-Panasiuk Natalia et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 10 (39) -
Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity.
Butera Yvan et al. Nature communications 2021 10 (1) 5705 -
Genetic characterization of West Nile Virus strains during neuroinvasives infection outbreak in Tunisia, 2018.
Fares Wasfi et al. Transboundary and emerging diseases 2020 11 (4) 2414-2421 -
Molecular epidemiologic characteristics of hemagglutinin from five waves of avian influenza A (H7N9) virus infection, from 2013 to 2017, in Zhejiang Province, China.
Sun Yi et al. Archives of virology 2021 10 -
Chikungunya viruses containing the A226V mutation detected retrospectively in Cameroon form a new geographical subclade.
Agbodzi Bright et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 10
PATHOGENICITY / ANTIMICROBIAL RESISTANCE
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Trajectory of genetic alterations associated with colistin resistance in Acinetobacter baumannii during an in-hospital outbreak of infection.
Yoon Eun-Jeong et al. The Journal of antimicrobial chemotherapy 2021 10 -
Genotypic and Phenotypic Characterization of Antimicrobial Resistance Profiles in Non-typhoidal Salmonella enterica Strains Isolated From Cambodian Informal Markets.
Schwan Carla L et al. Frontiers in microbiology 2021 10 711472 -
Expansion of KPC-producing Enterobacterales in four large hospitals in Hanoi, Vietnam.
Linh Tran Dieu et al. Journal of global antimicrobial resistance 2021 10 -
A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage.
AbuOun Manal et al. Microbial genomics 2021 10 (10) -
Genome-Wide Association Study Reveals Genetic Markers for Antimicrobial Resistance in Mycoplasma bovis.
Bokma Jade et al. Microbiology spectrum 2021 10 e0026221 -
Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya.
Kariuki Samuel et al. eLife 2021 9 -
Whole genome sequencing for surveillance of tuberculosis drug resistance and determination of resistant level in China.
Liu Dongxin et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2021 10 -
The biological and clinical significance of emerging SARS-CoV-2 variants
Tao K, et al. Nat Rev Genet, Sep 17, 2021.
DETECTION / DIAGNOSIS
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An economic evaluation of the Whole Genome Sequencing source tracking program in the U.S.
Brown Brad et al. PloS one 2021 10 (10) e0258262 -
Supplementing SARS-CoV-2 genomic surveillance with PCR-based variant detection for real-time actionable information, the Netherlands, June to July 2021
Molenkamp R, et al. Eurosurveillance, Oct 7, 2021. -
Aerosol SARS-CoV-2 in hospitals and long-term care homes during the COVID-19 pandemic.
Mallach Gary et al. PloS one 2021 10 (9) e0258151 -
Duration of Viral Nucleic Acid Shedding and Early Reinfection With Severe Respiratory Syndrome Coronavirus 2 in Healthcare Workers and First Responders.
Brad J Biggerstaff et al. J Infect Dis 2021 10 (11) 1873-1877 -
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.
O'Toole Áine et al. Wellcome open research 2021 10 121 -
Imported human norovirus in travelers, Shanghai port, China 2018: An epidemiological and whole genome sequencing study
Zhang Z, et al. Travel Med Infect Dis, Oct 2021. -
Genotyping Cyclospora cayetanensis from multiple outbreak clusters with an emphasis on a cluster linked to bagged salad mix - United States, 2020.
Barratt Joel et al. The Journal of infectious diseases 2021 10 -
Morphological, molecular and MALDI-TOF MS identification of ticks and tick-associated pathogens in Vietnam.
Huynh Ly Na et al. PLoS neglected tropical diseases 2021 9 (9) e0009813
EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION
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Regional outbreak of multidrug-resistant Klebsiella pneumoniae carbapenemase-producing Pseudomonas Aeruginosa.
Bekana K Tadese et al. Infect Control Hosp Epidemiol 2021 10 (1) 96-98 -
Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks.
Li Shaoting et al. Nature communications 2021 8 (1) 5109 -
Mycobacterium chimaera infections among cardiothoracic surgery patients associated with heater-cooler devices-Kansas and California, 2019.
Kerui Xu et al. Infect Control Hosp Epidemiol 2021 10 (10) 1333-1338 -
Genomic characterization and phylogenetic analysis of the first SARS-CoV-2 variants introduced in Lebanon.
Feghali Rita et al. PeerJ 2021 10 e11015 -
Nosocomial outbreak caused by the SARS-CoV-2 Delta variant in a highly vaccinated population, Israel, July 2021.
Shitrit Pnina et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 10 (39) -
Genomic epidemiological analysis of SARS-CoV-2 household transmission.
Hare Daniel et al. Access microbiology 2021 10 (7) 000252 -
The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study.
Boshier Florencia A T et al. The Journal of infection 2021 10 -
The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities.
Aggarwal Dinesh et al. The Lancet. Microbe 2021 10 -
Transmission of SARS-CoV-2 during a 2-h domestic flight to Okinawa, Japan, March 2020.
Toyokawa Takao et al. Influenza and other respiratory viruses 2021 10 -
Genomic investigation of a household SARS-CoV-2 disease cluster in Arizona involving a cat, dog, and pet owner.
Yaglom Hayley D et al. One health (Amsterdam, Netherlands) 2021 10 100333 -
The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.
López Mariana G et al. Nature genetics 2021 10 (10) 1405-1414 -
Outbreaks of mumps genotype G viruses in the Netherlands between October 2019 and March 2020: clusters associated with multiple introductions.
Shah Anita A et al. BMC infectious diseases 2021 10 (1) 1035
ANTIMICROBIALS / VACCINES / INTERVENTIONS
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The impact of SARS-CoV-2 vaccination on Alpha and Delta variant transmission
Eyre DW, et al. medRxiv, Sep 29, 2021. -
No Significant Difference in Viral Load Between Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Groups Infected with SARS-CoV-2 Delta Variant
Acharya CB, et al. medRxiv, Sep 29, 2021. -
Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants
Bruxvoort KJ, et al. medRxiv, Oct 1, 2021. -
The Delta Variant Had Negligible Impact on COVID-19 Vaccine Effectiveness in the USA
Blaiszik B, et al. medRxiv, Oct 2, 2021. -
An observational study of breakthrough SARS-CoV-2 Delta variant infections among vaccinated healthcare workers in Vietnam.
Chau Nguyen Van Vinh et al. EClinicalMedicine 2021 10 101143 -
Effectiveness of mRNA BNT162b2 COVID-19 vaccine up to 6 months in a large integrated health system in the USA: a retrospective cohort study
Tartof SY, et al. Lancet, Oct 4, 2021. -
Waning of BNT162b2 Vaccine Protection against SARS-CoV-2 Infection in Qatar.
Chemaitelly Hiam et al. The New England journal of medicine 2021 10 -
Effectiveness of Covid-19 Vaccines in Ambulatory and Inpatient Care Settings
Thompson MG, et al. New Engl J Med, Oct 7, 2021. -
Fecal shedding of two novel live attenuated oral poliovirus type 2 vaccines candidates by healthy bOPV/IPV-vaccinated infants: two randomized clinical trials.
Gast Christopher et al. The Journal of infectious diseases 2021 10
HOST-MICROBE INTERACTIONS
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A MUC5B gene polymorphism, rs35705950-T, confers protective effects in COVID-19 infection
Verma A, et al. medRxiv, Sep 29, 2021. -
COVID-19 in twins: What can we learn from them
Castro MV, et al. medRxiv, Oct 2, 2021. -
Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae
Thompson RC, et al. medRxiv, Oct 5, 2021. -
Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality.
Nakanishi Tomoko et al. The Journal of clinical investigation 2021 10 -
Genetic Susceptibility to Pneumonia: A GWAS Meta-Analysis Between the UK Biobank and FinnGen.
Campos Adrian I et al. Twin research and human genetics : the official journal of the International Society for Twin Studies 2021 8 (3) 145-154
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:Apr 18, 2024
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