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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Feb 25, 2021
NEWS

How Deadly Is the U.K. Variant?
Walker M. MedPage Today, Feb 14, 2021.

California's coronavirus strain looks increasingly dangerous: 'The devil is already here'
Healy M. Los Angeles Times, Feb 23, 2021.

California coronavirus strain may be more infectious--and lethal
Wadman M. Science, Feb 23, 2021.

Report Outlines Strategy for Surveillance of Emerging Coronavirus Variants
Stephenson J. JAMA Network, Feb 23, 2021.

A New Coronavirus Variant Is Spreading in New York, Researchers Report
Mandavilli A. New York Times, Feb 24, 2021.

Global 'Force' to Track Viral Variants
GenomeWeb, Feb 23, 2021.

Superspreading drives the COVID pandemic--and could help to tame it
Lewis D. Nature, Feb 23, 2021.

FDA says Covid vaccines that target new variants won't need large clinical trials to win approval
Lovelace Jr B. CNBC, Feb 22, 2021.

Moderna ready to test version of Covid-19 vaccine aimed at worrisome variant
Garde D, Herper M. STAT, Feb 24, 2021.



CONCEPTS / COMMENTSY

Emerging infections and the integrative environment-health sciences: the road ahead. Fisher Matthew C et al. Nature reviews. Microbiology 2021 Jan

A universal coronavirus vaccine. Koff Wayne C et al. Science (New York, N.Y.) 2021 Feb (6531) 759

Insights from SARS-CoV-2 sequences. Martin Michael A et al. Science (New York, N.Y.) 2021 01 (6528) 466-467

The Recombination Potential between SARS-CoV-2 and MERS-CoV from Cross-Species Spill-over Infections. Sajini Abdulrahim A et al. Journal of epidemiology and global health 2021 2

Ten simple rules for getting started with command-line bioinformatics. Brandies Parice A et al. PLoS computational biology 2021 2 (2) e1008645



EVOLUTION / ECOLOGY / POPULATIONS

Molecular characterization of invasive serogroup B Neisseria meningitidis isolates from Spain during 2015-2018: evolution of the vaccine antigen factor H binding protein (FHbp). Abad Raquel et al. The Journal of infection 2021 Feb

Evolution and circulation of Yersinia pestis in the Northern Caspian and Northern Aral Sea regions in the 20th-21st centuries. Eroshenko Galina A et al. PloS one 2021 2 (2) e0244615

Genomic diversity of Salmonella enterica - The UoWUCC 10K genomes project Achtman Mark et al. Wellcome open research 2021 2 223

Population Biology and Comparative Genomics of Campylobacter Species. Epping Lennard et al. Current topics in microbiology and immunology 2021 2 59-78

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts Tasakis RN, et al. bioRxiv, Feb 19, 2021.

Predicting the zoonotic capacity of mammal species for SARS-CoV-2. Fischhoff Ilya R et al. bioRxiv : the preprint server for biology 2021 2

Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants Tchesnokova V, et al. bioRxiv, Feb 22, 2021.

One Year of SARS-CoV-2 Evolution Wu A, et al. Cell Host Microbe, Feb 19, 2021.

Characterizing SARS-CoV-2 genome diversity circulating in South American countries: signatures of potentially emergent lineages? Munoz M, et al. Int J Infect Dis, Feb 20, 2021.

Comparative genomics reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2. Chiara Matteo et al. Molecular biology and evolution 2021 2

Role of mutational reversions and fitness restoration in Zika virus spread to the Americas. Liu Jianying et al. Nature communications 2021 1 (1) 595

Population bottlenecks and founder effects: implications for mosquito-borne arboviral emergence. Weaver Scott C et al. Nature reviews. Microbiology 2021 1 (3) 184-195

A machine-learning approach to map landscape connectivity in Aedes aegypti with genetic and environmental data Pless E, et al. PNAS March 2, 2021 118 (9) e2003201118


PATHOGENICITY / ANTIMICROBIAL RESISTANC

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile. Bravo Veronica et al. PLoS neglected tropical diseases 2021 Feb (2) e0009207

Phylogeny, recombination, and invasiveness of group B Streptococcus revealed by genomic comparisons of its global strains. Lin Enze et al. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2020 10 (3) 581-590

Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil Nonaka CK, et al. Emerg Infect Dis, Feb 19, 2021.

Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil. Nonaka Carolina K V et al. Emerging infectious diseases 2021 2 (5)

Evidence that a naturally occurring single nucleotide polymorphism in the RagC gene of Leishmania donovani contributes to reduced virulence. Lypaczewski Patrick et al. PLoS neglected tropical diseases 2021 2 (2) e0009079


DETECTION / DIAGNOSIS

Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review. Weis C V et al. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2020 Oct (10) 1310-1317 Brand

Progress Report: Next-Generation Sequencing (NGS), Multiplex Polymerase Chain Reaction (PCR), and Broad-Range Molecular Assays as Diagnostic Tools for Fever of Unknown Origin (FUO) Investigations in Adults. Wright William F et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 Feb

A real-time multiplex PCR assay for detection of the causative agents of rat bite fever, Streptobacillus moniliformis and zoonoticStreptobacillus species. Kelly Aubree J et al. Diagnostic microbiology and infectious disease 2021 2 (2) 115335 Brand

Could mutations of SARS-CoV-2 suppress diagnostic detection? Ascoli Carl A et al. Nature biotechnology 2021 2

Clinical and Laboratory Findings in Patients with Potential SARS-CoV-2 Reinfection, May-July 2020. Lee James T et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 2

First Identified Cases of SARS-CoV-2 Variant B.1.1.7 in Minnesota--December 2020-January 2021 Firestone MJ, et al. MMWR, Feb 26, 2021.

Detection of B.1.351 SARS-CoV-2 Variant Strain--Zambia, December 2020 Mwenda M, et al. MMWR, Feb 26, 2021.

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing. Bhoyar Rahul C et al. PloS one 2021 2 (2) e0247115

Wastewater Monitoring of SARS-CoV-2 from Acute Care Hospitals Identifies Nosocomial Transmission and Outbreaks Acosta N, et al. medRxiv, Feb 23, 2021.

Methodological Approach for Wastewater Based Epidemiological Studies for SARS-CoV-2 Kopperi H, et al. medRxiv, Feb 22, 2021.

An allele-specific primer extension assay to quantify the proportion of B.1.1.7-specific SARS-CoV-2 RNA in wastewater Graber TE, et al. medRxiv, Feb 23, 2021.

Rapid SARS-CoV-2 variants spread detected in France using specific RT-PCR testing Haim-Boukobza S, et al. medRxiv, Feb 23, 2021.

Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. Wylezich Claudia et al. Microbiome 2021 2 (1) 51

Endemic chikungunya fever in Kenyan children: a prospective cohort study. Nyamwaya Doris K et al. BMC infectious diseases 2021 2 (1) 186

Human infection with Seoul orthohantavirus in Korea, 2019. Kang Changmin et al. PLoS neglected tropical diseases 2021 2 (2) e0009168 Brand

Genomic investigation of atypical malaria cases in Kanel, northern Senegal. Sy Mouhamad et al. Malaria journal 2021 2 (1) 103 Brand

From 18S to 28S rRNA Gene: An Improved Targeted Sarcocystidae PCR Amplification, Species Identification with Long DNA Sequences. Lee Florence C H et al. The American journal of tropical medicine and hygiene 2021 2

Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome. Chng Lena et al. PLoS neglected tropical diseases 2021 2 (2) e0009149


EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

An outbreak investigation of Legionella non- pneumophila Legionnaires' disease in Sweden, April to August 2018: Gardening and use of commercial bagged soil associated with infections. Löf Emma et al. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2021 Feb (7) Brand

Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care. Roberts Leah W et al. Microbial genomics 2021 Feb Brand

Estimating the spreading and dominance of SARS-CoV-2 VOC 202012/01 (lineage B.1.1.7) across Europe Gozzi N, et al. medRxiv, Feb 23, 2021.

Early pandemic molecular diversity of SARS-CoV-2 in children. Moustafa Ahmed M et al. medRxiv : the preprint server for health sciences 2021 2

Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States. Alpert Tara et al. medRxiv : the preprint server for health sciences 2021 2

Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak Masoli J, et al. medRxiv, Feb 19, 2021.

Characterization of acute HCV infection and transmission networks in people who currently inject drugs in Catalonia: usefulness of dried blood spots. Antuori A et al. Hepatology (Baltimore, Md.) 2021 2



HOST-MICROBE INTERACTIONS

Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects. Maldonado Lucas L et al. Scientific reports 2021 Feb (1) 4108

A genomic region associated with protection against severe COVID-19 is inherited from Neandertals. Zeberg Hugo et al. Proceedings of the National Academy of Sciences of the United States of America 2021 2 (9)


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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