Pathogen Advanced Molecular Detection Database|Archive|PHGKB

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Public Health Genomics and Precision Health Knowledge Base (v8.9)

Pathogen Advanced Molecular Detection Database|Archive|PHGKB

Advanced Molecular Detection Clips Content (Published on 06/10/2021)

News
Concepts / Comments
Methods / Tools
Evolution / Ecology / Populations
Pathogenicity / Antimicrobial Resistance
Detection / Diagnosis
Epidemiology / Outbreaks / Transmission
Antimicrobials / Vaccines / Interventions
Host-Microbe Interactions

NEWS

Study shows nearly 50,000 live animals on sale in China's Wuhan before COVID-19 began
Reuters, Jun 9, 2021.
As India's pandemic surge eases, a race begins to prepare for a possible next wave
Massih N, Dutta T. Washington Post, Jun 9, 2021.
The Fundamental Question of the Pandemic is Shifting
Yong E. Atlantic, Jun 9, 2021.
The COVID lab-leak hypothesis: what scientists do and don't know
Maxmen A, Mallapaty S. Nature, Jun 8, 2021.
Covid-19: Delta variant is now UK's most dominant strain and spreading through schools.
Torjesen Ingrid et al. BMJ (Clinical research ed.) 2021 6 n1445
More transmissible, wilier variant makes Covid-19 vaccinations even more crucial, experts say
Joseph A. STAT, Jun 10, 2021.
How the "Alpha" Coronavirus Variant Became So Powerful
Zimmer C. New York Times, June 7, 2021.
Delta variant accounts for 6 percent of new U.S. coronavirus infections
Bernstein L. Washington Post, June 8, 2021.
?Nanotraps? Designed to Capture and Clear SARS-CoV-2
Abbasi J. JAMA, Jun 8, 2021.
A "landmark" trial to test mRNA vaccines against COVID-19 in Africa can't get the coveted shots
Cohen J. Science, Jun 7, 2021.
With a souped up synthetic genome, scientists make bacteria impervious to viral attack
Molteni M. STAT, Jun 3, 2021.
The Disease Detective--Joe DeRisi
Kahn J. New York Times, Jun 3, 2021.
Would you have your DNA tested to predict how hard COVID-19 would strike? Should you?
Kaiser J. Science, Jun 7, 2021.
Fecal Microbiota Transplantation is Poised for a Makeover
Williams S. The Scientist, Jun 1, 2021.

CONCEPTS / COMMENTS

Come on, CDC, we need you
Thorp H. Science, Jun 4, 2021.
What I Learned in 33 Years at the C.D.C.
Shuchat A. New York Times, Jun 10, 2021.
40 years of AIDS taught us epidemiologic humility. We need to apply that lesson in fighting Covid-19
Mayer KH. STAT, June 4, 2021.
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
Konings F, et al. Nat Microbiol, Jun 9, 2021.
Identifying and Tracking SARS-CoV-2 Variants - A Challenge and an Opportunity.
Becker Scott J et al. The New England journal of medicine 2021 6
Embrace the WHO's new naming system for coronavirus variants
(editorial) Nature, Jun 9, 2021.
Bird Flu Outbreak Amidst COVID-19 Pandemic in South Africa: Efforts and Challenges at Hand.
Uwishema Olivier et al. Journal of medical virology 2021 6
Environmental Risk Assessment of Recombinant Viral Vector Vaccines against SARS-Cov-2.
Baldo Aline et al. Vaccines 2021 6 (5)
Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network.
Colella Jocelyn P et al. PLoS pathogens 2021 6 (6) e1009583
HIPAA and the Leak of "Deidentified" EHR Data
Mandl KD, Perakslis ED. New Engl J Med, Jun 10, 2021.

METHODS / TOOLS

Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens
Kuchinski KS, et al. medRxiv, Jun 4, 2021.
Detecting SARS-CoV-2 and its variant strains with a full genome tiling array.
Jiang Limin et al. Briefings in bioinformatics 2021 6
Centralised or Localised Pathogen Whole Genome Sequencing: Lessons Learnt From Implementation in a Clinical Diagnostic Laboratory.
Beukers Alicia G et al. Frontiers in cellular and infection microbiology 2021 6 636290
Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing Data
Ellmen I, et al. medRxiv, Jun 6, 2021.
A virtual biobank for companion animals: A parvovirus pilot study.
Smith Shirley L et al. The Veterinary record 2021 6 e556

EVOLUTION / ECOLOGY / POPULATIONS

Genomic analysis of Clostridioides difficile in two regions of the United States reveals a diversity of strains and limited transmission.

Pecora Nicole et al. The Journal of infectious diseases 2021 6
Coronavirus surveillance in wildlife from two Congo basin countries detects RNA of multiple species circulating in bats and rodents.

Kumakamba Charles et al. PloS one 2021 6 (6) e0236971
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.

Marotz Clarisse et al. Microbiome 2021 6 (1) 132
Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020-May 2021.

Paul Prabasaj et al. MMWR. Morbidity and mortality weekly report 2021 6 (23) 846-850
2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline

Capoferri AA, et al. medRxiv, Jun 4, 2021.
Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection

Karim F, et al. medRxiv, Jun 4, 2021.
The total number and mass of SARS-CoV-2 virions

Sender R, et al. eProc Nat Acad Sci, Jun 22, 2021.
An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India.

Yadav Pragya D et al. Viruses 2021 6 (5)
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.

Hodcroft Emma B et al. Nature 2021 6
Detection of R.1 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with spike protein W152L/E484K/G769V mutations in Japan.

Hirotsu Yosuke et al. PLoS pathogens 2021 6 (6) e1009619
Genomic Epidemiology of SARS-CoV-2 From Mainland China With Newly Obtained Genomes From Henan Province.

Song Ning et al. Frontiers in microbiology 2021 6 673855
SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions.

Timmers Luis Fernando Saraiva Macedo et al. Scientific reports 2021 6 (1) 11998
Molecular diversity and evolution of bat group C betacoronaviruses: origin of the novel human group C betacoronavirus (abridged secondary publication).

Lau S K P et al. Hong Kong medical journal = Xianggang yi xue za zhi 2021 6 (3) 23-27
Emergence of the E484K Mutation in SARS-CoV-2 Lineage B.1.1.345 in Upstate New York.

Lesho Emil et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 6
Coxsackievirus B4: an underestimated pathogen associated with a hand, foot, and mouth disease outbreak.

Xiao Jinbo et al. Archives of virology 2021 6
Molecular ecology of Triatoma dimidiata in southern Belize reveals risk for human infection and the local differentiation of Trypanosoma cruzi parasites.

Polonio Roy et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 6

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance.
Wang Wei et al. mSystems 2021 6 e0118520
Highly transmitted M. tuberculosis strains are more likely to evolve MDR/XDR and cause outbreaks, but what makes them highly transmitted?
Alame Emane Amel Kevin et al. Tuberculosis (Edinburgh, Scotland) 2021 6 102092
Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers.
D'Souza Alaric W et al. Genome medicine 2021 6 (1) 79
Structural dynamics of SARS-CoV-2 variants: a health monitoring strategy for anticipating Covid-19 outbreaks.
Fantini Jacques et al. The Journal of infection 2021 6
Phenotypic and genetic characterization of MERS coronaviruses from Africa to understand their zoonotic potential.
Zhou Ziqi et al. Proceedings of the National Academy of Sciences of the United States of America 2021 6 (25)

DETECTION / DIAGNOSIS

The African Network for Improved Diagnostics, Epidemiology and Management of common infectious Agents.
Schubert Grit et al. BMC infectious diseases 2021 6 (1) 539
Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai.
Miao Qing et al. Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi 2021 6
Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England
Challen R, et al. medRxiv, Jun 7, 2021.
SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay.
Buck Michael D et al. Wellcome open research 2021 6 9
FnCas9 based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV2 variants on a paper strip.
Kumar Manoj et al. eLife 2021 6
SARS-CoV-2 RNAemia and proteomic trajectories inform prognostication in COVID-19 patients admitted to intensive care
Gutmann C, et al. Nat Commun. 2021 Jun 7;12(1):3406.
The first case study of wastewater-based epidemiology of COVID-19 in Hong Kong.
Xu Xiaoqing et al. The Science of the total environment 2021 6 148000
Rapid diagnostic tests to address challenges for global measles surveillance.
Brown David W et al. Current opinion in virology 2020 7 77-84
Measuring transfer of human norovirus during sandwich production: Simulating the role of food, food handlers and the environment.
Derrick Jade et al. International journal of food microbiology 2021 5 109151

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Improvements to the Success of Outbreak Investigations of Legionnaires' Disease: 40 Years of Testing and Investigation in New York State
Schoonmaker-Bopp D, et al. Appl Environ Microbiol. 2021 Jun 4;AEM0058021.
Whole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019
Joensen KG, et al. Euro Surveill. 2021 Jun;26(22).
Outbreak of SARS-CoV-2 B.1.1.7 Lineage after Vaccination in Long-Term Care Facility, Germany, February-March 2021
Tober-Lau P, et al. Emerg Infect Dis, Jun 8, 2021.
Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec.
Paré Bastien et al. medRxiv : the preprint server for health sciences 2021 6
Adverse Outcomes Associated with SARS-CoV-2 variant B.1.351 Infection in Vaccinated Residents of a Long Term Care Home, Ontario, Canada.
Vanker Ahmed et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 6
Ct Values do not Predict SARS-CoV-2 Transmissibility in College Students.
Tian Di et al. The Journal of molecular diagnostics : JMD 2021 6
Increased household secondary attacks rates with Variant of Concern SARS-CoV-2 index cases.
Buchan Sarah A et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 6
Inferring SARS-CoV-2 RNA shedding into wastewater relative to time of infection
Cavany SM, et al. medRxiv, Jun 6, 2021.
Healthcare workers acquired COVID-19 disease from patients? An investigation by phylogenomics.
Chun-Wai Wong River et al. The Journal of hospital infection 2021 6
Virology features of a family cluster of SARS-CoV-2 infections in Shanghai, China.
Zhou Yanqiu et al. Biosafety and health 2021 6

ANTIMICROBIALS / VACCINES / INTERVENTIONS

Delayed Antibody and T-Cell Response to BNT162b2 Vaccination in the Elderly, Germany
Schwarz T, et al. Emerg Infect Dis, Jun 8, 2021.
Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants.
Xu Jianliang et al. Nature 2021 6
Neutralization against B.1.351 and B.1.617.2 with sera of COVID-19 recovered cases and vaccinees of BBV152
Yadav PD, et al. bioRxiv, Jun 7, 2021.
Vaccine Breakthrough Infections with SARS-CoV-2 Variants.
Hacisuleyman Ezgi et al. The New England journal of medicine 2021 4 (23) 2212-2218
Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom
Pritchard E, et al. Nat Med, Jun 9, 2021.
SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD and S2
Amanat F, et al. Cell, Jun 8, 2021.
A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T-cell responses
Tauzin A, et al. Cell Host Microbe, Jun 7, 2021.
Nasal delivery of an IgM offers broad protection from SARS-CoV-2 variants.
Ku Zhiqiang et al. Nature 2021 6
Immunogenicity of Ad26.COV2.S vaccine against SARS-CoV-2 variants in humans.
Alter Galit et al. Nature 2021 6

HOST-MICROBE INTERACTIONS

Blood RNA signature RISK4LEP predicts leprosy years before clinical onset.
Tió-Coma Maria et al. EBioMedicine 2021 6 103379
Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species
Wang R, et al. Immunity, Jun 8, 2021.
A catalog of associations between rare coding variants and COVID-19 outcomes
Kosmicki JA, et al. medRxiv, Feb 27, 2021.
Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals
Kosmicki JA, et al. Am J Hum Genet, Jun 3, 2021.
Vitamin D and COVID-19 susceptibility and severity in the COVID-19 Host Genetics Initiative: A Mendelian randomization study.
Butler-Laporte Guillaume et al. PLoS medicine 2021 6 (6) e1003605
Do monogenic inborn errors of immunity cause susceptibility to severe COVID-19?
Cotsapas Chris et al. The Journal of clinical investigation 2021 6

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 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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