Phylogeny News and Research

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Phylogenetic analysis explores the evolutionary relationships between organisms and is a vital foundation for microbial studies. The development of reliable phylogenetic trees is an important step in developing new treatments and discovering the origins of eukaryotes, prokaryotes and archaea.

Scientists hypothesize SARS-CoV-2 cryptically circulating among humans before the current outbreak

As nations begin to recover, researchers from the National Taiwan University and Academia Sinica in Taipei have been looking to identify the changes the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underwent over the course of the pandemic in order to better understand why the disease showed such virulence.

20 Sep 2021

What impact has SARS-CoV-2 variant B.1.1.519 had on Mexico City?

The current study reports the effective reproduction number of B.1.1.519 and presents its geographical origin based on phylogenetic analysis.

20 Sep 2021

A variant analysis approach for SARS-CoV-2 in wastewater samples

A recent study proposes a simple and specific method for the enhanced detection of the SARS-CoV-2 VOCs in wastewater samples.

19 Sep 2021

Potential variant of interest in South Africa assigned to the PANGO lineage C.1.2

Continual genomic surveillance of the SARS-CoV-2 strains in South Africa has revealed an increase in the number of sequences belonging to C.1 lineage during the third wave (May 2021) of SARS-CoV-2 infections. This observation was unexpected because C.1 was last reported in January 2021.

26 Aug 2021

New phylogenomic platform identifies increased recombination rates in SARS-CoV-2

Researchers in the United States, Australia and the UK have developed a novel method that enables the evolutionary ancestry (phylogeny) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to be comprehensively searched for recombinant lineages.

8 Aug 2021

Purifying selection drives time-dependency of short-term mutation rates in SARS-CoV-2 and pH1N1 influenza

A new paper, available on the medRxiv* preprint server, indicates the adaptation undergone by the SARS-CoV-2 molecular genome and the pH1N1 influenza pandemic strain during the first year of their spread, separately. Using statistical and phylogenetic skills, the researchers present a picture of the emergence, rates of change, and of growth, of these two viruses as time passes.

3 Aug 2021

CoVizu: Making visual sense of variation in SARS-CoV-2 genomes

A new study proposes a solution to this problem in the form of a new method that can both evaluate and visually represent high numbers of SARS-CoV-2 genomes.

25 Jul 2021

How SARS-CoV-2 has evolved over the course of the pandemic

In an effort to understand the ongoing evolution of the SARS-CoV-2 genome, researchers constructed a phylogenetic tree of all available SARS-CoV-2 genomes.

7 Jul 2021

Is the SARS-CoV-2 delta variant threatening vaccine efficacy?

A new study in the UK, by researchers at Imperial College London, The Francis Crick Institute and the University of Glasgow, explores the loss of coronavirus disease 2019 (COVID-19) vaccine efficacy against the virus behind the current pandemic caused by the emergence of newer variants that have undergone mutational escape.

30 Jun 2021

Scientists predict driver mutations of future SARS-CoV-2 variants of concern

A team of scientists from the USA has recently predicted the driver mutations that may appear in future variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The prediction is based on currently available genetic surveillance data on amino acid mutations present in SARS-CoV-2 variants. A detailed description of the study is currently available on the medRxiv* preprint server.

24 Jun 2021

New study suggests an earlier and faster spread of COVID-19 than initially thought

Researchers from Kent University in the UK have shown that the first coronavirus disease (COVID-19) patient likely dates back to October 2019. They also found that the spread to other continents of its causative pathogen – the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – occurred faster and sooner.

24 Jun 2021

Is B.1.617.2 more transmissible than earlier SARS-CoV-2 variants?

A new study, released as a preprint on the medRxiv* server, reports that the B.1.617.2 variant is possibly more transmissible than earlier variants, based on the discovery that the serial intervals were not prolonged with this strain.

10 Jun 2021

SARS-CoV-2 B.1.1.345 variant carrying E484K mutation detected in New York

The report, published in the journal Clinical Infectious Diseases, revealed that the variant detected has been spreading at an alarming rate since November. By February 2021, it accounted for 12.3 percent of all cases in the area.

8 Jun 2021

Could a mathematical application of information theory identify and predict SARS-CoV-2 mutations?

An interesting new study by researchers at the University of Portsmouth, UK, describes the use of a mathematical method to sequence genomes based on information theory. The method offers an alternative to clinical techniques, allowing mutations to be detected and possibly even predicted. In this way, it opens new research opportunities in bioinformatics and genetics.

31 May 2021

Researchers identify a novel SARS-CoV-2 variant (with the V1230L mutation) in West Bengal, India

Researchers analyzed 2,000 viral genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the causative agent of coronavirus disease 2019 (COVID-19) – sequences obtained from India and found a new variant that could be more infectious and transmissible.

28 May 2021

North America has 87% of all unique SARS-CoV-2 S protein variants in the NCBI database among six continents

Recently, a team of researchers from various countries analyzed the unique variants of S proteins across six continents, including Africa, Asia, Oceania, Europe, South America, and North America. They wanted to characterize the unique S protein variants embedded in SARS-CoV-2 genomes infecting millions of people globally.

20 May 2021

SARS-CoV-2 variant spread study in France shows B.1.351/V2 variant outgrowing B.1.1.7/V1 variant

A recent study by researchers in France has compared the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern. The team found a significant transmission advantage of V2 (from lineage B.1.351) over V1 (from lineage B.1.1.7). A pre-print version of the research paper is available on the medRxiv* server.

20 May 2021

Immunity developed by SARS-CoV-2 infection can protect against E484K variants, suggests study

A team of scientists from Japan has recently investigated the neutralizing potency of convalescent sera against currently circulating SARS-CoV-2 variants with multiple spike mutations.

13 May 2021

Spread of minority SARS-CoV-2 variants in New York City

Viruses mutate to survive. But not all mutations are beneficial to the virus. On the other hand, some mutations such as N501Y and E484K on the spike protein propelled specific severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to ‘variant of concern’ status, due to their ability to increase transmission and weaken the response of neutralizing antibodies.

12 May 2021

The travel-related origin and spread of SARS-CoV-2 B.1.620 strain

A new preprint research paper posted to the medRxiv* server describes a new variant B.1.620, which appeared in Lithuania, and is now prevalent in several countries in Europe, as well as in central Africa.

11 May 2021