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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Mar 4, 2021
NEWS

The Secret Life of a Coronavirus
Zimmer C. New York Times, Feb 26, 2021.

Hackers Break Into 'Biochemical Systems' At Oxford University Lab Studying Covid-19
Brewster T. Forbes, Feb 25, 2021.

Where did COVID come from? Five mysteries that remain
Mallapaty S. Nature, Feb 26, 2021.

The search for animals harbouring coronavirus -- and why it matters
Mallapaty S. Nature, Mar 2, 2021.

The short-term, middle-term, and long-term future of the coronavirus
Joseaph A, Branswell H. STAT, Mar 4, 2021.

Brazil's Covid Crisis Is a Warning to the Whole World, Scientists Say
Andreoni M, et al. New York Times, Mar 3, 2021.

Virus Variant in Brazil Infected Many Who Had Already Recovered From Covid-19
Zimmer C. New York Times, Mar 1, 2021.

'Everything Seems So Tenuous': Variants Threaten N.Y.C.'s Progress on Virus
Otterman S. New York Times, Feb 25, 2021.

Why Virus Variants Have Such Weird Names
Mandavilli A, Mueller B. New York Times, Mar 2, 2021.

Massive Google-funded COVID database will track variants and immunity
Maxmen A. Nature, Feb 24, 2021.

MDH Tracking 14 COVID 'Vaccine Breakthrough Cases'; All Had Mild Or No Symptoms
Raddatz K. CBS Minnesota, Mar 3, 2021.


EVENTS / TRAINING / WEB RESOURCES

Visualisation tools to help understand SARS-CoV-2 mutations
(blog post) COVID-19 Genomics UK Consortium (COG-UK)

COG-UK Mutation Explorer
(website) COVID-19 Genomics UK (COG-UK), last updated Feb 25, 2021.

An interactive website tracking COVID-19 vaccine development
Shrotri M, et al. Lancet Global Health, Mar 2, 2021.

COVID-19 Vaccine Tracker
LSHTM Vaccine Centre, last update Mar 1, 2021.

The Predictive Power of Poop: COVID-19 Wastewater Surveillance to Inform Public Health Decisions in Colorado
(webinar) GenomeWeb, Mar 16, 2021, 1:00 pm EDT.



CONCEPTS / COMMENTSY

Want to track pandemic variants faster? Fix the bioinformatics bottleneck. Hodcroft Emma B et al. Nature 2021 3 (7848) 30-33 Brand

Spot the variant?the pursuit of greater vigilance (editorial) Lancet Microbe, March 2021.

The FDA's Experience with Covid-19 Antibody Tests. Shuren Jeffrey et al. The New England journal of medicine 2021 2 (7) 592-594

Human challenge trials to assess the efficacy of currently approved COVID-19 vaccines against SARS-CoV-2 variants. Su Shan et al. Emerging microbes & infections 2021 2 1-7

COVID vaccination studies: plan now to pool data, or be bogged down in confusion Dean N. Nature, Mar 3, 2021.

SARS-CoV-2 dependence on host pathways Wong JP, Damania B. Science, Feb 26, 2021.

A CRISPR response to pandemics?: Exploring the ethics of genetically engineering the human immune system. Germani Federico et al. EMBO reports 2021 2 (3) e52319


METHODS / TOOLS

Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Bogaerts Bert et al. Microbial genomics 2021 3

Toolkit for Quickly Generating and Characterizing Molecular Probes Specific for SARS-CoV-2 Nucleocapsid as a Primer for Future Coronavirus Pandemic Preparedness. Sherwood Laura Jo et al. ACS synthetic biology 2021 2 (2) 379-390

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation. Charre Caroline et al. Virus evolution 2020 12 (2) veaa075 Brand

Uncertainties in estimating SARS-CoV-2 prevalence by wastewater-based epidemiology. Li Xuan et al. Chemical engineering journal (Lausanne, Switzerland : 1996) 2021 3 129039

Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples. Teyssier Noam B et al. Malaria journal 2021 2 (1) 116


EVOLUTION / ECOLOGY / POPULATIONS

Population Genomic Analysis of Listeria monocytogenes From Food Reveals Substrate-Specific Genome Variation Bechtel Tyler D et al. Frontiers in microbiology 2021 2 620033

A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York Annavajhala MK, et al. medRxiv, Feb 25, 2021.

Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck. Braun Katarina M et al. PLoS pathogens 2021 2 (2) e1009373

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Francisco Ronaldo da Silva et al. Virus research 2021 2 198345

Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern Long SW, et al. medRxiv, Mar 2, 2021.

Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil Tosta S, et al. medRxiv, Mar 1, 2021.

Persistent SARS-CoV-2 infection and increasing viral variants in children and young adults with impaired humoral immunity Truong TT, et al. medRxiv, Mar 3, 2021.

Introductions and evolutions of SARS-CoV-2 strains in Japan Tokumasu R, et al. medRxiv, Mar 2, 2021. Brand

SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection Choudhary MC, et al. medRxiv, Mar 3, 2021.

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil Faria NR, et al. medRxiv, Mar 3, 2021.

Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil. Iani Felipe C M et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 3 104785

Genomic characterization of 99 viruses from the bunyavirus families Nairoviridae, Peribunyaviridae, and Phenuiviridae, including 35 previously unsequenced viruses. Kapuscinski Marylee L et al. PLoS pathogens 2021 3 (3) e1009315 Brand

Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018. Cheng Wenjun et al. Archives of virology 2021 2

New genotype invasion of dengue virus serotype 1 drove massive outbreak in Guangzhou, China. Ma Mengmeng et al. Parasites & vectors 2021 3 (1) 126

Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents. Tonkin-Hill Gerry et al. PLoS genetics 2021 2 (2) e1009269

The influence of roads on the fine-scale population genetic structure of the dengue vector Aedes aegypti (Linnaeus). Regilme Maria Angenica F et al. PLoS neglected tropical diseases 2021 2 (2) e0009139


PATHOGENICITY / ANTIMICROBIAL RESISTANC

Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire. Penna Bruno et al. Scientific reports 2021 2 (1) 4724

Population structure and genetic diversity of non-O157 Shiga toxin-producing Escherichia coli (STEC) clinical isolates from Michigan. Blankenship Heather M et al. Scientific reports 2021 2 (1) 4461

Colistin Heteroresistance Is Largely Undetected among Carbapenem-Resistant Enterobacterales in the United States Band Victor I et al. mBio 2021 1 (1)

Genomic investigation of antimicrobial resistance determinants and virulence factors in Salmonella enterica serovars isolated from contaminated food and human stool samples in Brazil. de Melo Adma Nadja Ferreira et al. International journal of food microbiology 2021 2 109091

SARS-CoV-2 spike D614G change enhances replication and transmission. Zhou Bin et al. Nature 2021 2 Brand

Increased hazard of mortality in cases compatible with SARS-CoV-2 variant of concern 202012/1 - a matched cohort study Challen R, et al. medRxiv, Feb 27, 2021.

Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19. Nakamichi Kenji et al. Scientific reports 2021 2 (1) 4802

SARS-CoV-2 genomic surveillance identifies naturally occurring truncations of ORF7a that limit immune suppression. Nemudryi Artem et al. medRxiv : the preprint server for health sciences 2021 3


DETECTION / DIAGNOSIS

Genomic surveillance and improved molecular typing of Bordetella pertussis using wgMLST Weigand Michael R et al. Journal of clinical microbiology 2021 2 Brand

Detection of Tick-borne Bacteria from Whole Blood Using 16S Ribosomal RNA Gene PCR Followed by Next-Generation Sequencing. Rodino Kyle G et al. Journal of clinical microbiology 2021 2 Brand

A review of the presence of SARS-CoV-2 RNA in wastewater and airborne particulates and its use for virus spreading surveillance. Anand Uttpal et al. Environmental research 2021 3 110929 Brand

In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19. Phan Isabelle Q et al. Scientific reports 2021 2 (1) 4290

RT-qPCR assay for detection of British (B.1.1.7) and South Africa (B.1.351) variants of SARS-CoV-2 Yaniv K, et al. medRxiv, Mar 1, 2021.

SARS-CoV-2 Total and Subgenomic RNA Viral Load in Hospitalized Patients Dimcheff DE, et al. medRxiv, Mar 1, 2021.

First Identified Cases of SARS-CoV-2 Variant P.1 in the United States -- Minnesota, January 2021 Firestone MJ, et al. MMWR, Mar 3, 2021. Brand Brand

SARS-CoV-2 Early Screening at the Point of Entry: Travelers From Bangladesh to Italy-July 2020. Rueca Martina et al. Frontiers in genetics 2021 2 625607 Brand

High-Throughput Wastewater SARS-CoV-2 Detection Enables Forecasting of Community Infection Dynamics in San Diego County. Karthikeyan Smruthi et al. mSystems 2021 3 (2)

Persistent SARS-CoV-2 RNA Shedding without Evidence of Infectiousness: A Cohort Study of Individuals with COVID-19. Owusu Daniel et al. The Journal of infectious diseases 2021 3

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis Coil DA, et al. medRxiv, Feb 24, 2021.

A Metagenomic Analysis of Mosquito Virome Collected From Different Animal Farms at Yunnan-Myanmar Border of China. Hameed Muddassar et al. Frontiers in microbiology 2021 2 591478

Co-Infections: Simultaneous Detections of West Nile Virus and Usutu Virus in Birds from Germany. Santos Pauline Dianne et al. Transboundary and emerging diseases 2021 3

Concordance of genotypic resistance interpretation algorithms in HIV-1 infected patients: An exploratory analysis in Greece. Kantzanou Maria et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2021 3 104779 Brand

Reassortant Cache Valley virus associated with acute febrile, non-neurologic illness, Missouri. Baker Molly et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 2 Brand Brand


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Hospital-acquired Legionella Pneumonia Outbreak at an Academic Medical Center: Lessons Learned. Kessler Michael A et al. American journal of infection control 2021 2 Brand

A statewide analysis of SARS-CoV-2 transmission in New York Lasek-Nesselquist E, et al. medRxiv, Feb 27, 2021.

Utility of whole genome sequencing during an investigation of multiple foodborne outbreaks of Shigella sonnei Mikhail AF, et al. Epidemiol Infect, Mar 1, 2021. Brand

Autochthonous and Travel Acquired Hepatitis E Virus in Australia. O'Keefe Jacinta et al. Frontiers in microbiology 2021 2 640325

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. Washington Nicole L et al. medRxiv : the preprint server for health sciences 2021 2

High prevalence of SARS-CoV-2 antibodies in care homes affected by COVID-19: Prospective cohort study, England. Ladhani Shamez N et al. EClinicalMedicine 2020 11 100597

Genomic epidemiology of COVID-19 in care homes in the East of England. Hamilton William L et al. eLife 2021 3

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England Davies NG, et al. Science, Mar 3, 2021.

Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco Peng J, et al. medRxiv, Mar 3, 2021.

Travel from the United Kingdom to the United States by a Symptomatic Patient Infected with the SARS-CoV-2 B.1.1.7 Variant --Texas, January 2021 Ojelade M, et al. MMWR, Mar 3, 2021.

Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole genome sequencing. Løvestad Alexander Hesselberg et al. The Journal of hospital infection 2021 3 Brand

SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak. Loureiro Carmen L et al. PloS one 2021 2 (2) e0247196

Novel Mutation of SARS-CoV-2, Vietnam, July 2020. Phuong Hoang Vu Mai et al. Emerging infectious diseases 2021 3 (5) Brand

Outbreak of hepatitis B and hepatitis C virus infections associated with a cardiology clinic, West Virginia, 2012-2014. Tressler Stacy R et al. Infection control and hospital epidemiology 2021 3 1-6 Brand


ANTIMICROBIALS / VACCINES / INTERVENTIONS

Evaluation of a SARS-CoV-2 Vaccine NVX-CoV2373 in Younger and Older Adults Formica N, et al. medRxiv, Mar 1, 2021.


HOST-MICROBE INTERACTIONS

The Variant Gambit: COVID's Next Move Plante JA, et al. Cell Host Microbe, Mar 1, 2021.

Genetic variation of IFNL4 is associated with COVID-19 Saponi-Cortes JM, et al. medRxiv, Mar 4, 2021.

Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection. Dobrindt Kristina et al. Stem cell reports 2021 2

Shorter androgen receptor polyQ alleles protect against life-threatening COVID-19 disease in European males. Baldassarri Margherita et al. EBioMedicine 2021 3 103246

High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion Geyer PE, et al. medRxiv, Feb 23, 2021.


Note: Brand indicates that at least one CDC-affiliated author; Brand indicates that the article addresses aspects of implementation or evaluation in clinical or public health practice.

About Weekly AMD Clips

Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged. Items marked I&E address aspects of implementation or evaluation in clinical or public health practice.


Disclaimer: Articles listed in the Public Health Knowledge Base are selected by the CDC Office of Public Health Genomics to provide current awareness of the literature and news. Inclusion in the update 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 update, 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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