Distinct mutations and lineages of SARS‐CoV‐2 virus in the early phase of COVID‐19 pandemic and subsequent one‐year global expansion

Abstract A novel coronavirus, SARS-CoV-2, has caused over 85 million cases and over 1.8 million deaths worldwide since it occurred twelve months ago in Wuhan, China. Here we conceptualized the time-series evolutionary and expansion dynamics of SARS-CoV-2 by taking a series of cross-sectional view of viral genomes from early outbreak in January in Wuhan to early phase of global ignition in early April, and finally to the subsequent global expansion by late December 2020. By scrutinizing cases from early outbreak, we found a viral genotype from the Seafood Market in Wuhan featured with two concurrent mutations has become the overwhelmingly dominant genotype (95.3%) of the pandemic. By analyzing 4,013 full-length SARS-CoV-2 genomes from different continents by early April, we were able to visualize the genomic diversity over a 14-week timespan since the outbreak in Wuhan. 2,954 unique nucleotide substitutions were identified with 31 of the 4,013 genomes remaining as ancestral type, and 952 (32.2%) mutations recurred in more than one genome. 11 major viral genotypes with unique geographic distributions were identified. As the pandemic has been unfolding for more than one year, we also used the same approach to analyze 261,323 full-length SARS-CoV-2 genomes from the world since the outbreak in Wuhan (i.e. including all the available viral genomes in the GISAID database as of 25 December 2020) in order to recapitulate our findings in a real-time fashion and to present a full catalogue of SARS-CoV-2 mutations. We demonstrated the viral genotypic dynamics from different geographic locations over one-year timespan reveal transmission routes and indicate subsequent expansion. This study, to our knowledge, is heretofore the largest and most comprehensive genomic study of SARS-CoV-2. It indicates the viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures. Moreover, the dynamics of viral mutational spectrum in the study may help the early identification of new strains in patients to reduce further spread of infection, and guide the development of molecular diagnosis and vaccines against COVID-19, and last but not the least help assess their accuracy and efficacy.

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Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent global expansion

10.1101/2021.01.05.425339 ◽

2021 ◽

Author(s):

Yan Chen ◽

Shiyong Li ◽

Wei Wu ◽

Shuaipeng Geng ◽

Mao Mao

Keyword(s):

Early Phase ◽

Full Length ◽

Control Measures ◽

Viral Genotype ◽

Nucleotide Substitutions ◽

Viral Genomes ◽

One Year ◽

Novel Coronavirus ◽

Dominant Genotype ◽

Ancestral Type

A novel coronavirus, SARS-CoV-2, has caused over 85 million cases and over 1.8 million deaths worldwide since it occurred twelve months ago in Wuhan, China. Here we first analyzed 4,013 full-length SARS-CoV-2 genomes from different continents over a 14-week timespan since the outbreak in Wuhan. 2,954 unique nucleotide substitutions were identified with 31 of the 4,013 genomes remaining as ancestral type, and 952 (32.2%) mutations recurred in more than one genome. A viral genotype from the Seafood Market in Wuhan featured with two concurrent mutations was the dominant genotype (80.9%) of the pandemic. We also identified unique genotypic compositions from different geographic locations, and time-series viral genotypic dynamics in the early phase that reveal transmission routes and subsequent expansion. In the end, as the pandemic has been unfolding for more than one year, we also used the same approach to analyze 261,350 full-length SARS-CoV-2 genomes from the world since the outbreak in Wuhan (i.e. all the available viral genomes in the GISAID database as of 25 December 2020) in order to recapitulate our findings in a real-time fashion. Our study indicates the viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures.

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Between ‘Savage Man’ and ‘Most Faithful Englishman’ Manteo and the Early Anglo-Indian Exchange, 1584–1590

Itinerario ◽

10.1017/s0165115300044545 ◽

2000 ◽

Vol 24 (2) ◽

pp. 146-169 ◽

Cited By ~ 1

Author(s):

Michael Leroy Oberg

Keyword(s):

North Carolina ◽

Chesapeake Bay ◽

One Year ◽

Anglo Indian

In August of 1587 Manteo, an Indian from Croatoan Island, joined a group of English settlers in an attack on the native village of Dasemunkepeuc, located on the coast of present-day North Carolina. These colonists, amongst whom Manteo lived, had landed on Roanoke Island less than a month before, dumped there by a pilot more interested in hunting Spanish prize ships than in carrying colonists to their intended place of settlement along the Chesapeake Bay. The colonists had hoped to re-establish peaceful relations with area natives, and for that reason they relied upon Manteo to act as an interpreter, broker, and intercultural diplomat. The legacy of Anglo-Indian bitterness remaining from Ralph Lane's military settlement, however, which had hastily abandoned the island one year before, was too great for Manteo to overcome. The settlers found themselves that summer in the midst of hostile Indians.

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Some Biological Applications of High Voltage Electron Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051505 ◽

1974 ◽

Vol 32 ◽

pp. 298-299

Author(s):

Hans Ris

Keyword(s):

High Voltage ◽

Chromosome Structure ◽

Nerve Fibers ◽

Good Resolution ◽

High Voltage Electron Microscopy ◽

Voltage Electron ◽

University Of Wisconsin ◽

High Voltage Electron ◽

One Year ◽

The University

The High Voltage Electron Microscope Laboratory at the University of Wisconsin has been in operation a little over one year. I would like to give a progress report about our experience with this new technique. The achievement of good resolution with thick specimens has been mainly exploited so far. A cold stage which will allow us to look at frozen specimens and a hydration stage are now being installed in our microscope. This will soon make it possible to study undehydrated specimens, a particularly exciting application of the high voltage microscope.Some of the problems studied at the Madison facility are: Structure of kinetoplast and flagella in trypanosomes (J. Paulin, U. of Georgia); growth cones of nerve fibers (R. Hannah, U. of Georgia Medical School); spiny dendrites in cerebellum of mouse (Scott and Guillery, Anatomy, U. of Wis.); spindle of baker's yeast (Joan Peterson, Madison) spindle of Haemanthus (A. Bajer, U. of Oregon, Eugene) chromosome structure (Hans Ris, U. of Wisconsin, Madison). Dr. Paulin and Dr. Hanna are reporting their work separately at this meeting and I shall therefore not discuss it here.

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Osseointegration interface of calcified bone and endosseous implants

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100130110 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1096-1097

Author(s):

K.E. Krizan ◽

J.E. Laffoon ◽

M.J. Buckley

Keyword(s):

Structure And Function ◽

Titanium Implants ◽

En Bloc ◽

Endosseous Implants ◽

Ultrastructural Studies ◽

The Past ◽

Cacodylate Buffer ◽

One Year ◽

And Function

With increase use of tissue-integrated prostheses in recent years it is a goal to understand what is happening at the interface between haversion bone and bulk metal. This study uses electron microscopy (EM) techniques to establish parameters for osseointegration (structure and function between bone and nonload-carrying implants) in an animal model. In the past the interface has been evaluated extensively with light microscopy methods. Today researchers are using the EM for ultrastructural studies of the bone tissue and implant responses to an in vivo environment. Under general anesthesia nine adult mongrel dogs received three Brånemark (Nobelpharma) 3.75 × 7 mm titanium implants surgical placed in their left zygomatic arch. After a one year healing period the animals were injected with a routine bone marker (oxytetracycline), euthanized and perfused via aortic cannulation with 3% glutaraldehyde in 0.1M cacodylate buffer pH 7.2. Implants were retrieved en bloc, harvest radiographs made (Fig. 1), and routinely embedded in plastic. Tissue and implants were cut into 300 micron thick wafers, longitudinally to the implant with an Isomet saw and diamond wafering blade [Beuhler] until the center of the implant was reached.

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Effectiveness of a 24-hour nicotine patch in conjunction with a cognitive behavioural programme: one year outcome transdermal

Addiction ◽

10.1046/j.1360-0443.1997.921274.x ◽

1997 ◽

Vol 92 (1) ◽

pp. 27-31

Author(s):

Robyn L. Richmond ◽

Linda Kehoe ◽

Abilio Cesar De Almeida Neto

Keyword(s):

Nicotine Patch ◽

Cognitive Behavioural ◽

One Year

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Resources: Internet Resources for the Independent Medical Evaluator – 2007

Guides Newsletter ◽

10.1001/amaguidesnewsletters.2007.julaug02 ◽

2007 ◽

Vol 12 (4) ◽

pp. 4-7

Author(s):

Christopher R. Brigham ◽

Jenny Walker

Keyword(s):

Head Trauma ◽

Clonic Seizure ◽

Acute Subdural Hematoma ◽

Orbital Fracture ◽

Orbital Wall ◽

First Occurrence ◽

One Year ◽

The One ◽

Neurological Injuries ◽

Medial Orbital Wall

Abstract Rating patients with head trauma and multiple neurological injuries can be challenging. The AMA Guides to the Evaluation of Permanent Impairment (AMA Guides), Fifth Edition, Section 13.2, Criteria for Rating Impairment Due to Central Nervous System Disorders, outlines the process to rate impairment due to head trauma. This article summarizes the case of a 57-year-old male security guard who presents with headache, decreased sensation on the left cheek, loss of sense of smell, and problems with memory, among other symptoms. One year ago the patient was assaulted while on the job: his Glasgow Coma Score was 14; he had left periorbital ecchymosis and a 2.5 cm laceration over the left eyelid; a small right temporoparietal acute subdural hematoma; left inferior and medial orbital wall fractures; and, four hours after admission to the hospital, he experienced a generalized tonic-clonic seizure. This patient's impairment must include the following components: single seizure, orbital fracture, infraorbital neuropathy, anosmia, headache, and memory complaints. The article shows how the ratable impairments are combined using the Combining Impairment Ratings section. Because this patient has not experienced any seizures since the first occurrence, according to the AMA Guides he is not experiencing the “episodic neurological impairments” required for disability. Complex cases such as the one presented here highlight the need to use the criteria and estimates that are located in several sections of the AMA Guides.

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