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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Jun 17, 2021
NEWS

Rockefeller Foundation Funds Global Pathogen Sequencing With $20M, Forms Collaborations
GenomeWeb, Jun 10, 2021.

Fifty-nine labs around world handle the deadliest pathogens - only a quarter score high on safety
Lentzos F, Koblenz G. The Conversation, Jun 14, 2021.

NIH study suggests coronavirus may have been in U.S. as early as December 2019
Achenbach J. Washington Post, Jun 15, 2021.

Sequencing Study Uncovers MERS-Related Coronavirus in Swiss Bats
GenomeWeb, Jun 16, 2021.

A Top Virologist in China, at Center of a Pandemic Storm, Speaks Out
Qin A, Buckley C. New York Times, Jun 14, 2021.

Sewage sleuths helped an Arizona town beat back Covid-19. For wastewater epidemiology, that's just the start
Molteni M. STAT, Jul 16, 2021.

CureVac, latest experimental coronavirus vaccine, proved just 47 percent effective amid spread of variants, preliminary analysis shows
Johnson CY. Washington Post, Jun 16, 2021.

Novavax Offers U.S. a Fourth Strong Covid-19 Vaccine
Zimmer C. New York Times, Jun 14, 2021.

A long-term perspective on immunity to COVID
Radbruch A, Chang HD. Nature, Jun 14, 2021.


CONCEPTS / COMMENTS

Early Laboratory Preparedness of the Korea Disease Control and Prevention Agency and Response to Unknown Pneumonia Outbreak from Wuhan, China, in January 2020. Kim Il-Hwan et al. Annals of laboratory medicine 2021 6 (6) 532-539 Brand

Leveraging artificial intelligence for pandemic preparedness and response: a scoping review to identify key use cases. Syrowatka Ania et al. NPJ digital medicine 2021 6 (1) 96

How the COVID pandemic is changing global science collaborations Maher B, Van Noorden R. Nature, Jun 16, 2021.

Zoonotic and Reverse Zoonotic Transmissibility of SARS-CoV-2. Goraichuk Iryna V et al. Virus research 2021 6 198473

Will SARS-CoV-2 variants of concern affect the promise of vaccines? Gupta Ravindra K et al. Nature reviews. Immunology 2021 5 (6) 340-341

Test it earlier, result it faster, makes us stronger: how rapid viral diagnostics enable therapeutic success. Greninger Alexander L et al. Current opinion in virology 2021 6 111-116


METHODS / TOOLS

Topology identifies emerging adaptive mutations in SARS-CoV-2 Bleher M, et al. medRxiv, Jun 13, 2021.

Computational Analysis and Phylogenetic Clustering of SARS-CoV-2 Genomes. Jolly Bani et al. Bio-protocol 2021 6 (8) e3999

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Sserwadda Ivan et al. Microbial genomics 2021 6 (6) Brand

A versatile reverse genetics platform for SARS-CoV-2 and other positive-strand RNA viruses. Amarilla Alberto A et al. Nature communications 2021 6 (1) 3431

Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities. Dippenaar Anzaan et al. Journal of clinical microbiology 2021 6 JCM0064621 Brand

Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data. Lüftinger Lukas et al. Frontiers in cellular and infection microbiology 2021 3 610348


EVOLUTION / ECOLOGY / POPULATIONS

Three transmission events of Vibrio cholerae O1 into Lusaka, Zambia. Mwaba John et al. BMC infectious diseases 2021 6 (1) 570

Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. Knight Daniel R et al. eLife 2021 6

Population analysis of Vibrio cholerae in aquatic reservoirs reveals a novel sister species (Vibrio paracholerae sp. nov.) with a history of association with humans. Islam Mohammad Tarequl et al. Applied and environmental microbiology 2021 6 AEM0042221 Brand

Potential transmission chains of variant B.1.1.7 and co-mutations of SARS-CoV-2. Zhang Jingsong et al. Cell discovery 2021 6 (1) 44

Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations. Shen Lishuang et al. Emerging microbes & infections 2021 6 1-13

SARS-CoV-2 in wastewater from Mexico City used for irrigation in the Mezquital Valley: quantification and modelling of geographic dispersion Coronado Y, et al. medRxiv, Jun 12, 2021.

SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States. Cai Hugh Y et al. Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc 2021 6 10406387211023481

Genetic evolution and transmission dynamics of clade 2.3.2.1a highly pathogenic avian influenza A/H5N1 viruses in Bangladesh. Kwon Jung-Hoon et al. Virus evolution 2021 6 (2) veaa046


PATHOGENICITY / ANTIMICROBIAL RESISTANC

Antimicrobial resistance and molecular epidemiological typing of Neisseria gonorrhoeae isolates from Kyrgyzstan in Central Asia, 2012 and 2017. Karymbaeva Saliya et al. BMC infectious diseases 2021 6 (1) 559

Risk of hospital admission for patients with SARS-CoV-2 variant B.1.1.7: cohort analysis. Nyberg Tommy et al. BMJ (Clinical research ed.) 2021 6 n1412

The SARS-CoV-2 mRNA vaccine breakthrough infection phenotype includes significant symptoms, live virus shedding, and viral genetic diversity. Pollett Simon D et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 6


DETECTION / DIAGNOSIS

Salmonella Genomics in Public Health and Food Safety. Brown Eric W et al. EcoSal Plus 2021 6 eESP00082020 Brand

Rapid detection of human origin colistin-resistance genes mcr-1, mcr-3, mcr-8, mcr-10 in clinical fecal samples. Hu Shuangfang et al. Archives of microbiology 2021 6

Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens. Jain Komal et al. Scientific reports 2021 6 (1) 12384

Utility of whole genome sequencing in assessing and enhancing partner notification of Neisseria gonorrhoeae infection. Kong Ling Yuan et al. Sexually transmitted diseases 2021 6 Brand

A portable magnetofluidic platform for detecting sexually transmitted infections and antimicrobial susceptibility. Trick Alexander Y et al. Science translational medicine 2021 5 (593)

Wastewater-based epidemiology for tracking COVID-19 trend and variants of concern in Ohio, United States Ai Y, et al. medRxiv, Jun 10, 2021. Brand

High throughput sequencing based detection of SARS-CoV-2 prevailing in wastewater of Pune, West India Dharmadhikari T, et al. medRxiv, Jun 9, 2021.

Operationalizing a routine wastewater monitoring laboratory for SARS-CoV-2 Kantor RS, et al. medRxiv, Jun 9, 2021. Brand

Molecular benchmarks of a SARS-CoV-2 epidemic. Jonsson Hakon et al. Nature communications 2021 6 (1) 3633

Coupling freedom from disease principles and early warning from wastewater surveillance to improve health security Larsen DA, et al. medRxiv, Jun 14, 2021. Brand

Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave. Hernandez Matthew M et al. Nature communications 2021 6 (1) 3463

Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021. Wilton Thomas et al. mSystems 2021 6 e0035321

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 Brand

SYMPTOMATIC SARS-CoV-2 INFECTIONS AFTER FULL SCHEDULE BNT162b2 VACCINATION IN SEROPOSITIVE HEALTHCARE WORKERS: A CASE SERIES FROM A SINGLE INSTITUTION. Baj Andreina et al. Emerging microbes & infections 2021 6 1-6 Brand

RPAcan3990: an ultrasensitive recombinase polymerase assay to detect Angiostrongylus cantonensis DNA. Sears William J et al. Journal of clinical microbiology 2021 6 JCM0118521 Brand


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

Culture-independent genotyping revealed three strain clusters in a potential Neisseria gonorrhoeae outbreak in young heterosexuals (<25), the Netherlands, October 2017 to March 2019. van der Veer Brian M J W et al. Sexually transmitted diseases 2021 6 Brand

A tale of two variants: Spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in South Africa Althaus CL, et al. medRxiv, Jun 15, 2021.

Second wave of COVID-19 in India could be predicted with genomic surveillance of SARS-CoV-2 variants coupled with epidemiological data: A tool for future Kumar A, et al. medRxiv, Jun 13, 2021.

Recurrent Dissemination of SARS-CoV-2 Through the Uruguayan-Brazilian Border. Mir Daiana et al. Frontiers in microbiology 2021 6 653986

Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. Chappell Joseph G et al. The Journal of general virology 2021 6 (6)

Assessing the extent of community spread caused by mink-derived SARS-CoV-2 variants Wang L, et al. Innovation, Jun 7, 2021.

An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms Eckstrand C, et al. medRxiv, Jun 10, 2021.


ANTIMICROBIALS / VACCINES / INTERVENTIONS

Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom. Pritchard Emma et al. Nature medicine 2021 6 Brand

SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness Sheikh A, et al. Lancet, Jun 14, 2021. Brand

Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals. Kustin Talia et al. Nature medicine 2021 6

Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant Stowe J, et al. Public Health England, Jun 14,2021.

Safety, Immunogenicity, and Efficacy of a COVID-19 Vaccine (NVX-CoV2373) Co-administered With Seasonal Influenza Vaccines Toback S, et al. medRxiv, Jun 13, 2021.

BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants. Liu Jianying et al. Nature 2021 6

Spike D614G - A Candidate Vaccine Antigen Against Covid-19. Koenig Paul-Albert et al. The New England journal of medicine 2021 6 (24) 2349-2351


HOST-MICROBE INTERACTIONS

Switching Sides: How Endogenous Retroviruses Protect Us from Viral Infections. Srinivasachar Badarinarayan Smitha et al. Journal of virology 2021 4 (12)

AI-guided discovery of the invariant host response to viral pandemics. Sahoo Debashis et al. EBioMedicine 2021 6 103390

A year of COVID-19 GWAS results from the GRASP portal reveals potential SARS-CoV-2 modifiers Thibord F, et al. medRxiv, Jun 11, 2021.

A blood RNA transcriptome signature for COVID-19. Kwan Philip Kam Weng et al. BMC medical genomics 2021 6 (1) 155

Pan-ancestry exome-wide association analyses of COVID-19 outcomes in 586,157 individuals. Kosmicki Jack A et al. American journal of human genetics 2021 6

Will a little change do you good? A putative role of polymorphisms in COVID-19. Paim Adriana Alves Oliveira et al. Immunology letters 2021 4 9-14

Secretor status strongly influences the incidence of symptomatic norovirus infection in a genotype-dependent manner in a Nicaraguan birth cohort. Reyes Yaoska et al. The Journal of infectious diseases 2021 6 Brand Brand

Whole-exome sequencing reveals insights into genetic susceptibility to Congenital Zika Syndrome. Borda Victor et al. PLoS neglected tropical diseases 2021 6 (6) e0009507


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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