scholarly journals Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan

2021 ◽  
Vol 9 (12) ◽  
pp. 2609
Author(s):  
Atia Basheer ◽  
Imran Zahoor
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Reference Genome ◽  
Third Wave ◽  
Genomic Epidemiology ◽  
Wave Data ◽  
The World ◽  
Reference Sequences ◽  
First Time ◽  
Second Wave

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.

scholarly journals Genomic epidemiology of SARS-CoV-2 divulge B.1, B.1.36, and B.1.1.7 as the most dominant lineages in first, second, and third wave of SARS-CoV-2 infections in Pakistan

2021 ◽  
Author(s):  
Atia Basheer ◽  
Imran Zahoor
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Reference Genome ◽  
Third Wave ◽  
Genomic Epidemiology ◽  
Wave Data ◽  
The World ◽  
Reference Sequences ◽  
First Time ◽  
Second Wave

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with their role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3,804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain & coverage map was created by employing Nextclade. And by using the amino acid subsitutions the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following 7 clades G, GH, GR, GRY, L, O, & S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), & B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%) & B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of 9 lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), & Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.

The identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) among men who have sex with men in Jiangsu, China

2020 ◽  
Vol 18 ◽  
Author(s):  
Yin Yueqi ◽  
Zhou Ying ◽  
Lu Jing ◽  
Guo Hongxiong ◽  
Chen Jianshuang ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Second Generation ◽  
Emergency Situation ◽  
The World ◽  
Break Points ◽  
Sex With Men ◽  
Full Length Genome ◽  
Virus Strains ◽  
Hiv 1

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

scholarly journals Natural Patterns and Magnetic and Mental Processes of Coronavirus Activation and Neutralization

2022 ◽  
Vol 5 (2) ◽  
pp. 01-05
Author(s):  
Evgeny Bryndin
Keyword(s):  
Nobel Laureate ◽  
Third Wave ◽  
Mental Processes ◽  
The Third ◽  
The Past ◽  
The World ◽  
Mortality Increase ◽  
Repeated Infections ◽  
Second Wave ◽  
Seriously Ill

For twenty years, humanity has seen the third attempt at the transition of coronavirus to humans. The vaccine has been found, but coronavirus transitions will not stop even with the improvement of medicine. Nobel laureate in medicine Professor Luc Montagnier argues that vaccines may not live up to humanity's hopes of getting rid of COVID-19. Collective immunity for coronavirus has not been developed, repeated infections are more and more common, beds of seriously ill people are not empty, and mortality is running high, no one knows what will happen to all of us. In Israel, where vaccination has long been compulsory, and over 60% of the population, including underage children, have been vaccinated, the incidence is not just declining, but still breaking all records. So, the maximum number of cases here was revealed on September 1 - 16,629, which almost caught up with Russia (18,368 confirmed on the same September 1) with our percentage of vaccinated 26.1% of the number of citizens. At the end of September 2021, morbidity and mortality increase, because it is a system. Based on existing monthly pneumonia mortality statistics over the past 15 years, there are three waves each year. Since September 22, there has been a surge of pneumonia, ARI, and even non-communicable diseases. The second wave comes at the end of December - January, it is usually three times larger than the first. Then around March-April there is a third wave. These three waves exist steadily from year to year, their amplitudes can change, then one will be higher, then the other, they are not absolutely hard on schedule, but they are reproduced regularly in other countries. The first wave of the Spanish pandemic covered the world just at the end of September 1918. The coronavirus was the same. The first wave in America is September 2019, an unexplained surge of pneumonia with a rather high mortality rate, which was written off for smoking e-cigarettes and called "vape." Now they decided to watch the surviving tests of patients, and there - COVID-19. In Europe, it was the same.

Neuroexistentialism

2018 ◽  
Keyword(s):  
Moral Responsibility ◽  
Meaning In Life ◽  
Common Good ◽  
Religious Tradition ◽  
Third Wave ◽  
The Past ◽  
The World ◽  
The Common ◽  
The Mind ◽  
Second Wave

Existentialism is a concern about the foundation of meaning, morals, and purpose. Existentialisms arise when some foundation for these elements of being is under assault. In the past, first-wave existentialism concerned the increasingly apparent inability of religion and religious tradition to provide such a foundation, as typified in the writings of Kierkegaard, Dostoevsky, and Nietzsche. Second-wave existentialism, personified philosophically by Sartre, Camus, and de Beauvoir, developed in response to the inability of an overly optimistic Enlightenment vision of reason and the common good to provide such a foundation. There is a third-wave existentialism, a new existentialism, developing in response to advances in the neurosciences that threaten the last vestiges of an immaterial soul or self. With the increasing explanatory and therapeutic power of neuroscience, the mind no longer stands apart from the world to serve as a foundation of meaning. This produces foundational anxiety. This collection of new essays explores the anxiety caused by this third-wave existentialism and some responses to it. It brings together some of the world’s leading philosophers, neuroscientists, cognitive scientists, and legal scholars to tackle our neuroexistentialist predicament and explore what the mind sciences can tell us about morality, love, emotion, autonomy, consciousness, selfhood, free will, moral responsibility, law, the nature of criminal punishment, meaning in life, and purpose.

On Ukrainian Citizens as taxpayers in sociological measurements

2021 ◽  
pp. 156-180
Author(s):  
OLHA IVASHCHENKO ◽  
DMYTRO BOYARCHUK ◽  
YEVGEN SHULGA
Keyword(s):  
Financial Literacy ◽  
Sociological Research ◽  
Third Wave ◽  
State Budget ◽  
Level Of Knowledge ◽  
The Right ◽  
Taxation System ◽  
First Time ◽  
Second Wave

The article deals with the results of first special sociological research on taxpaying thematic undertaken in Ukraine. Three waves of national wide survey (N1 = 2038 F2F; N2/3 = 2000 CATI) during 2020 by means of questionnaire with 5 basic questions regarding the taxpaying theme: budget structure, main expenses clauses, evaluated free of charge state services, equitable tax level, taxes for purchases and services. The provided analyses gave opportunity to choose most valuable questions concerning the Ukrainian citizens financial literacy in order to construct the Index of taxation erudition which revealed extremely low level of knowledge of Ukrainians as taxpayers about active tax system, particularly the role of taxpayers in state budget formation, when only 32% in the first wave and 43% in third wave pointed the citizen’s contribution, 54% respondents has no idea about the type of acting taxation system on the background of 52% in first wave and 39% in second wave, who pointed the 10% personal tax fee dimension as desirable and equitable. Only 20% citizens pointed the right figures of tax paying for purchases and services, when 36,5% have no knowledge about this tax at all, Sociologically was first time noticed important fixation of 56% readiness for paying less taxes and needed service accounts by own, especially for medical care and education, in such way it was acknowledged that constitutional article of social state is under civic scrutiny. As final research task the algorithm of Index of taxpayer’s knowledge ability has been proposed for regular monitoring as also recommendation for further special thematic research development with proper media involvements.

scholarly journals Hybridization in Selected Species and Genera of Diaptomid Copepods in China

Water ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1181
Author(s):  
Hui-Ming Li ◽  
Ping Liu ◽  
Xiao-Li Zhang ◽  
Henri J. Dumont ◽  
Bo-Ping Han
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Genetic Distances ◽  
Intergeneric Hybridization ◽  
Cryptic Speciation ◽  
Calanoid Copepods ◽  
Mitochondrial Coi ◽  
Different Populations ◽  
First Time ◽  
Hybridization And Introgression

To better understand the fauna of freshwater calanoid copepods of China, including the occurrence of intra- and intergeneric hybridization, we studied five species, distributed across the whole of China or in South China. We sequenced a mitochondrial (COI) and the nuclear ribosome 18S operon (ITS) to reconstruct the phylogenetic trees by using a Bayesian and maximum likelihood (ML) approach with 161 individuals. The phylogeny tree revealed five clades and two geographically separated subclades in both S. ferus and P. tunguidus. We found, for the first time, that the hybrid specimens occurred in Diaptomidae, but low hybridization suggested effective barriers to hybridization and introgression. One hypothesis, that hybridization is recent and was initiated by invasions via canals built between the Yangtze and Pearl rivers c. 2000 years ago, is not supported by K2P genetic distances of the order of 20%. Furthermore, COI analysis of different populations of S. ferus and P. tunguidus revealed two geographical clades in each species, with genetic distances commensurate with cryptic speciation. Both clades occupy subranges maintained without visible barriers to mixis.

scholarly journals Anticipating Third Wave of Covid-19 in India. How Much Prepared We Are?

2021 ◽  
pp. 1-1
Author(s):  
Naveen Kumar
Keyword(s):  
Surveillance System ◽  
Essential Medicines ◽  
Third Wave ◽  
Age Group ◽  
Healthcare Facilities ◽  
Hospital Beds ◽  
The World ◽  
Spanish Flu ◽  
The Government ◽  
Second Wave

The second wave of Covid -19 in India has made us witness as to how negligence from the part of everyone of us, be it people, Government or policy makers of healthcare system might bring the unwanted disaster in the form of Covid Tsunami. This has made us to see never ending queues of patients , relatives standing for hours for the want of hospital beds, oxygen, essential medicines and lastly but unfortunate for their turn for the cremations of loved ones . But now we can see the number of active cases are declining across the country. Amidst this positive observation in regard of second wave ,there is speculation erupting about the Covid third wave. We can appreciate a similarity in the way that the noble corona virus behave with the Spanish flu that had shaken the world in 1918. It had resulted in three waves with second wave was most deadly and long lasting than the other two waves. During the first wave where the infection was mostly of mild severity we had seen the disease affecting the elderly and immune-compromised patients more. In contrast to this, second wave resulting from mutant strains affected the younger population more and it was of larger severity with high mortality rate. Scientists and experts are now anticipating the third wave , taking the lesson from the Spanish flu and we must be better prepare for it. In order to prepare ourselves from a expected third wave of Covid-19, we shouldn’t repeat mistakes that we made during previos waves. We should refrain ourselves from dismantling our enhanced healthcare facilities, there should not be any sorts of shortage of oxygen , hospital beds, and drug that we have already witnessed. We must have an aggressive containment measure comprising of a really strong and pro-active surveillance system. This can be achieved by increasing the capacity of the existing surveillance system by identifying active cases early. We must ensure that we should follow “social vaccine” of proper masking, avoid indoor gatherings, and proper sanitization. Our vaccination programme needs a boost. We should vaccinate a large section of people before any third wave hits us. The more we vaccinate, the better prepared we are. As medical professionals, it must be ensured that proper scientific protocol must be implemented while handling Covid-19 cases. And last but not the least efforts must be made to fill up vacancies seen in our public health system, especially for frontline healthcare workers. As it is anticipated that the young children are more vulnerable to the forthcoming third wave, efforts are to be sought in order to start vaccination of the younger children in our country. Trials for which has already been started in India and across the world. Till the time vaccine is made available, the resources are to be mobilized to build up healthcare facilities catering the vulnerable age group in this third wave such as building up of more paediatric wards, paediatric ICU’s , training of healthcare personals in handling the emergencies for expected third wave .In addition to these efforts , more and more paediatric covid care centers must be set up at various parts of the country. Equally important is making arrangements for rehabilitation centers for the orphans. Countries like US, Singapore and UAE have already started vaccinating the children in age group between 12 to 15 years with Pfizer-BioNTech Covid vaccine. It’s a high time that the government in India must consider for allowing “expedited approval pathway” to the companies like Pfizer for their Covid-19 vaccine for children. All these combined efforts from everyone may ensure that the country and world may remain well equipped against these subsequent waves of this deadly virus and pave the path of the triumph in the near future.

scholarly journals Africa’s COVID-19 third wave: A coupled behavior-disease system in a mutual feedback loop

2021 ◽  
Vol 2 (5) ◽  
pp. 26-30
Author(s):  
Jia Bainga Kangbai ◽  
◽  
Mahmoud Sheku ◽  
Braima Koroma ◽  
Joseph Mustapha Macathy ◽  
...  
Keyword(s):  
South Africa ◽  
Latin America ◽  
Feedback Loop ◽  
Third Wave ◽  
The Third ◽  
The World ◽  
Imported Cases ◽  
Second Wave

A year after COVID-19 was declared a pandemic much of the Africa continent started experiencing spikes in the number of COVID-19 cases and related deaths in what was referred to as the third wave of the pandemic. These spikes came right behind the heels of a second wave of the pandemic that barely went unnoticed in Africa. As of July 2021, Morocco, South Africa, Tunisia, Egypt, Nigeria, Libya, Kenya, Algeria, Zambia and Ethiopia accounted for approximately 86% of the reported increase in COVID-19; these countries were aptly described as being at the forefront of the continent’s third wave of the COVID-19 pandemic. Unlike those countries in Asia and Latin America that experienced what may generally being described as autochthonous COVID-19 third wave, Africa’s third wave COVID-19 cases are widely believed to have been triggered by imported cases. Africa like the rest of the world relaxed its COVID-19 restrictions almost at the same time; hence the continent’s spikes of COVID-19 cases and related deaths during the third wave of the pandemic have raised some questions.

scholarly journals Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches

2021 ◽  
Author(s):  
Bryan Thornlow ◽  
Cheng Ye ◽  
Nicola De Maio ◽  
Jakob McBroome ◽  
Angie S. Hinrichs ◽  
...  
Keyword(s):  
Public Health ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Computational Cost ◽  
Phylogenetic Inference ◽  
Contact Tracing ◽  
Genomic Epidemiology ◽  
Dense Sampling

AbstractPhylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 datasets do not fit this mould. There are currently over 5 million sequenced SARS-CoV-2 genomes in public databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an “online” approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between Likelihood and Parsimony approaches to phylogenetic inference. Maximum Likelihood (ML) methods are more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare. Therefore, it may be that approaches based on Maximum Parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger datasets. Here, we evaluate the performance of de novo and online phylogenetic approaches, and ML and MP frameworks, for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimizations produce more accurate SARS-CoV-2 phylogenies than do ML optimizations. Since MP is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo, we therefore propose that, in the context of comprehensive genomic epidemiology of SARS-CoV-2, MP online phylogenetics approaches should be favored.

scholarly journals First record of Xiphinema hunaniense Wang & Wu, 1992 (Dorylaimida: Longidoridae) associated with tea (Camellia sinensis (L.) Kuntze) in Thanh Hoa, Vietnam

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
Le Thi Mai Linh ◽  
Nguyen Huu Tien ◽  
Nguyen Thi Duyen ◽  
Trinh Quang Phap
Keyword(s):  
Camellia Sinensis ◽  
18S Rdna ◽  
Phylogenetic Trees ◽  
First Record ◽  
Cultivated Plants ◽  
Wide Range ◽  
The World ◽  
First Time ◽  
Ectoparasitic Nematodes ◽  
18S Rdna Sequence

The dagger nematodes, Xiphinema spp., are migratory root-ectoparasitic nematodes that cause damage to a wide range of wild and cultivated plants over the world. In Vietnam, this nematode group has been studied mainly based on morphological characterizations. During a survey of pathogens associated with tea, a plant with many medicinal and therapeutic potentials, a population of Xiphinema hunaniense was recorded. This study provides the first morphological and molecular characterizations of Xiphinema hunaniense found on Tea in Vietnam. The 28S rDNA, and 18S rDNA phylogenetic trees of the genus Xiphinema are also provided. 18S rDNA sequence of X. hunaniense is also submitted to GenBank for the first time. 

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