The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

Ciccozzi, Massimo; Lai, Alessia; Zehender, Gianguglielmo; Borsetti, Alessândra; Cella, Eleonora; Sagnelli, Caterina; Sagnelli, Caterina; Angeletti, Silvia

doi:10.1002/jmv.25526

Cited by 17 publications

(7 citation statements)

References 238 publications

(424 reference statements)

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“…In this study, phylogenetic analysis tools were utilized to assess origins, spread and mutations of SARS-CoV-2 in the MENA. Phylogeny construction can help to formulate hypotheses regarding the spread of certain taxa having a common origin (Ciccozzi et al, 2019;Pybus and Rambaut, 2009). In addition, molecular clock analysis can help to establish a timeline for origins of monophyletic clades (Jenkins et al, 2002;Nasir and Caetano-Anolles, 2015).…”

Section: Discussionmentioning

confidence: 99%

Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa

Sallam¹,

Ababneh²,

Dababseh³

et al. 2021

Heliyon

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Background: Phylogeny construction can help to reveal evolutionary relatedness among molecular sequences. The spike (S) gene of SARS-CoV-2 is the subject of an immune selective pressure which increases the variability in such region. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Another aim was to analyze the S gene sequences phylogenetically. Methods: The SARS-CoV-2 S gene sequences collected in the MENA were retrieved from the GISAID public database, together with its metadata. Mutation analysis was conducted in Molecular Evolutionary Genetics Analysis software. Phylogenetic analysis was done using maximum likelihood (ML) and Bayesian methods. Result: A total of 553 MENA sequences were analyzed and the most frequent S gene mutations included: D614G ¼ 435, Q677H ¼ 8, and V6F ¼ 5. A significant increase in the proportion of D614G was noticed from (63.0%) in February 2020, to (98.5%) in June 2020 (p < 0.001). Two large phylogenetic clusters were identified via ML analysis, which showed an evidence of inter-country mixing of sequences, which dated back to February 8, 2020 and March 15, 2020 (median estimates). The mean evolutionary rate for SARS-CoV-2 was about 6.5 Â 10 À3 substitutions/site/year based on large clusters' Bayesian analyses. Conclusions: The D614G mutation appeared to be taking over the COVID-19 infections in the MENA. Bayesian analysis suggested that SARS-CoV-2 might have been circulating in MENA earlier than previously reported.

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Section: Discussionmentioning

confidence: 99%

Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa

Sallam¹,

Ababneh²,

Dababseh³

et al. 2021

Heliyon

View full text Add to dashboard Cite

show abstract

“…In this study, phylogenetic analysis tools were utilized to assess origins, spread and mutations of SRAS-CoV-2 in the MENA. Phylogeny construction can help to formulate hypotheses regarding the spread of certain taxa having a common origin (Ciccozzi et al ., 2019; Pybus and Rambaut, 2009). In addition, molecular clock analysis can help to establish a timeline for origins of monophyletic clades (Jenkins et al ., 2002; Nasir and Caetano-Anolles, 2015).…”

Section: Discussionmentioning

confidence: 99%

Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study

Sallam

Ababneh

Dababseh

et al. 2020

Preprint

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Phylogeny construction can help to reveal evolutionary relatedness among molecular sequences. The spike (S) gene of SARS-CoV-2 is the subject of an immune selective pressure which increases the variability in such region. This study aimed to identify mutations in the S gene among SARS-CoV-2 sequences collected in the Middle East and North Africa (MENA), focusing on the D614G mutation, that has a presumed fitness advantage. Another aim was to analyze the S gene sequences phylogenetically. The SARS-CoV-2 S gene sequences collected in the MENA were retrieved from the GISAID public database, together with its metadata. Mutation analysis was conducted in Molecular Evolutionary Genetics Analysis software. Phylogenetic analysis was done using maximum likelihood (ML) and Bayesian methods. A total of 553 MENA sequences were analyzed and the most frequent S gene mutations included: D614G=435, Q677H=8, and V6F=5. A significant increase in the proportion of D614G was noticed from (63.0%) in February 2020, to (98.5%) in June 2020 (p<0.001). Two large phylogenetic clusters were identified via ML analysis, which showed an evidence of inter-country mixing of sequences, which dated back to February 8, 2020 and March 15, 2020 (median estimates). The mean evolutionary rate for SARS-CoV-2 was about 6.5 x 10-3 substitutions/site/year based on large clusters' Bayesian analyses. The D614G mutation appeared to be taking over the COVID-19 infections in the MENA. Bayesian analysis suggested that SARS-CoV-2 might have been circulating in MENA earlier than previously reported.

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“…Complications after a transplant can be related to the surgery itself (infection or abscess) or immunosuppressive therapy that the patient must continue for the life (cytomegalovirus [CMV] or viral infections) [5][6][7][8].…”

Section: Complications Related To Kidney Transplantationmentioning

confidence: 99%

Gastroenterological complications in kidney transplant patients

et al. 2020

Self Cite

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Kidney transplantation is the surgical operation by which one of the two original kidneys is replaced with another healthy one donated by a compatible individual. In most cases, donors are recently deceased. There is the possibility of withdrawing a kidney from a consenting living subject. Usually, living donors are direct family members, but they could be volunteers completely unrelated to the recipient. A much-feared complication in case of kidney transplantation is the appearance of infections. These tend to arise due to immune-suppressor drugs administered as anti-rejection therapy. In this review, we describe the gastrointestinal complications that can occur in subjects undergoing renal transplantation associated with secondary pathogenic microorganisms or due to mechanical injury during surgery or to metabolic or organic toxicity correlated to anti-rejection therapy. Some of these complications may compromise the quality of life or pose a significant risk of mortality; fortunately, many of them can be prevented and treated without the stopping the immunosuppression, thus avoiding the patient being exposed to the risk of rejection episodes.

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The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

Cited by 17 publications

References 238 publications

Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa

Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa

Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study

Gastroenterological complications in kidney transplant patients

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