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Advanced Molecular Detection Clips Database|AMD Clips|PHGKB

Pathogen Genomics and Health Database|AMD Clips|PHGKB
Publication Date: Sep 16, 2021

Did the coronavirus jump from animals to people twice?
Mallapaty S. Nature, Sep 16, 2021.

At the Tennessee state lab, genetic testing hunts for the next COVID-19 variant
Kelman B. Nashville Tennesseean, Sep 15, 2021.

United States boosts tracking of coronavirus strains as Mu variant draws scrutiny
Wadman M. Science, Sep 7, 2021.

The tangled history of mRNA vaccines
Dolgin E. Nature, Sep 14, 2021.

No revolution: COVID-19 boosted open access, but preprints are only a fraction of pandemic papers
Brainard J. Science, Sep 8, 2021.

2021 Ebola Outbreak Resulted From Viral Latency, Reactivation, Genomic Study Finds
GenomeWeb, Sep 15, 2021.

Ebola virus can lie low and reactivate after years in human survivors
Garry RF. Nature, Sep 15, 2021.

Two-dose J&J Ebola vaccine gives strong immune response
McLemon LM. CIDRAP, Sep 15, 2021.


Assessment of Genetic Stability During Serial In Vitro Passage and In Vivo Carriage. Sabol Ashley et al. Foodborne pathogens and disease 2021 9 Brand

Epidemiological Analysis of Salmonella enterica subsp. enterica Serovar Dublin in German Cattle Herds Using Whole-Genome Sequencing. García-Soto Silvia et al. Microbiology spectrum 2021 9 e0033221

Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar. Hasan Mohammad R et al. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2021 9

Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics Colson P, et al. medRxiv, Sep 12, 2021.

The evolutionary landscape of SARS-CoV-2 variant B.1.1.519 and its clinical impact in Mexico City Cedro-Tanda A, et al. medRxiv, Sep 14, 2021.

Comparative genomic analysis of genogroup 1 and genogroup 2 rotaviruses circulating in seven US cities, 2014-2016. Esona Mathew D et al. Virus evolution 2021 9 (1) veab023 Brand Brand

Infection, genetics, and evolution of Trichinella: Historical insights and applications to molecular epidemiology. Bilska-Zajac Ewa et al. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2021 9 105080


Prevalence, Serotypes, and Antimicrobial Resistance of Salmonella from Mink Feces and Feed in the United States. Agga Getahun E et al. Foodborne pathogens and disease 2021 9

Longitudinal Genomic Characterization of Carbapenemase-producing Enterobacteriaceae (CPE) Reveals Changing Pattern of CPEs Isolated in Hong Kong Hospitals. Zhu Chendi et al. International journal of antimicrobial agents 2021 9 106430

Impact of mutations in SARS-COV-2 spike on viral infectivity and antigenicity. Zhou Wenyang et al. Briefings in bioinformatics 2021 9

Breakthrough Infections of E484K-Harboring SARS-CoV-2 Delta Variant, Lombardy, Italy. Baj Andreina et al. Emerging infectious diseases 2021 9 (12)


Genomic epidemiology and strain taxonomy of Corynebacterium diphtheriae. Guglielmini Julien et al. Journal of clinical microbiology 2021 9 JCM0158121

Detection of Campylobacter jejuni diversity by clustered regularly interspaced short palindromic repeats (CRISPR) from an animal farm. Yeh Hung-Yueh et al. Veterinary medicine and science 2021 9

Comparison of RT-PCR Cycle Threshold Values from Respiratory Specimens in Symptomatic and Asymptomatic Children with SARS-CoV-2 Infection. Strutner John et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2021 9

Point-of-Care Toolkit for Multiplex Molecular Diagnosis of SARS-CoV-2 and Influenza A and B Viruses. Lee Dohwan et al. ACS sensors 2021 9

Landscape of SARS-CoV-2 genomic surveillance, public availability extent of genomic data, and epidemic shaped by variants: a global descriptive study Chen Z, et al. medRxiv, Sep 8, 2021. Brand

Nationwide trends in COVID-19 cases and SARS-CoV-2 wastewater concentrations in the United States Duvallet C, et al. medRxiv, Sep 12, 2021. Brand


Surveillance for Colonization, Transmission, and Infection With Methicillin-Susceptible Staphylococcus aureus in a Neonatal Intensive Care Unit. Nurjadi Dennis et al. JAMA network open 2021 9 (9) e2124938

Unexpected details regarding nosocomial transmission revealed by whole-genome sequencing of severe acute respiratory coronavirus virus 2 (SARS-CoV-2). Myhrman Sofia et al. Infection control and hospital epidemiology 2021 9 1-5

Bondi and beyond. Lessons from three waves of COVID-19 from 2020. Capon Adam et al. Public health research & practice 2021 9 (3) Brand

State-wide Genomic Epidemiology Investigations of COVID-19 Infections in Healthcare Workers--Insights for Future Pandemic Preparedness Watt AE, et al. medRxiv, Sep 13, 2021.

Genomics, social media and mobile phone data enable mapping of SARS-CoV-2 lineages to inform health policy in Bangladesh. Cowley Lauren A et al. Nature microbiology 2021 9

Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks Keita AK, et al. Nature, Sep 15, 2021.

Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters. Barratt Joel et al. Epidemiology and infection 2021 9 1-39 Brand Brand


Considerations in boosting COVID-19 vaccine immune responses Krause PR, et al. Lancet, Sep 13, 2021.

Safety and immunogenicity of SARS-CoV-2 variant mRNA vaccine boosters in healthy adults: an interim analysis Choi A, et al. Nat Med, Sep 15, 2021.

mRNA Vaccine Effectiveness against COVID-19 among Symptomatic Outpatients Aged ≥16 Years in the United States, February - May 2021. Kim Sara S et al. The Journal of infectious diseases 2021 9 Brand Brand

Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine through 6 Months. Thomas Stephen J et al. The New England journal of medicine 2021 9 Brand

Protection of BNT162b2 Vaccine Booster against Covid-19 in Israel. Bar-On Yinon M et al. The New England journal of medicine 2021 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.