Infection, Genetics and Evolution

IntroductionSARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemics. The virus crossed the species barrier and established in the human population due to its ability to exploit the ACE receptor for virus entry, which is present and abundant in several tissues, including the lung and respiratory tract, gastrointestinal tract and hearth. Virus interaction with the cellular receptor is mediated by the surface protein, known as Spike. Another structural protein of major importance in the Nucleocapsid, directly interacting with the viral RNA to form the ribonucleocapsid, considered a multifunctional protein, and being the target of the most molecular diagnostics assays. ObjectiveTo describe the frequency of substitutions in spike and nucleocapsid proteins of SARS-CoV-2 circulating in Colombia and evaluate the frequency of these substitutions in SARS-CoV-2 sequences from other countries of South America. Materials and methodsSamples of 43 patients were included for viral RNA detection by real-time RT-PCR using the Charite-Berlin protocol for the amplification of the SARS-CoV-2 E and RdRp genes. Genome sequences were obtained through the Oxford Nanopore and Illumina MiSeq technologies, following the artic.network "nCoV-2019 sequencing protocol". Available genomes were consulted from GISAID, GenBank, and Genome sequence archive (GSA) and a total of 371 genomes sequences from South America were included. The genome sequences were aligned with the Muscle tool using the MEGA X software. Substitution matrices of the Colombian sequences respect to the reference genome (NC_045512) at the nucleotide and amino acid levels were generated for the spike and nucleocapsid gene. Resultssubstitution D614G in the amino acid sequence of spike protein was found in 86.7% of the Colombian sequences; substitutions G181V and D936Y in 2.3%, respectively. Five substitutions were found in the nucleocapsid protein, with substitution R203K and G204R being the most frequent (13.95 %) in Colombia. The substitutions D614G in Spike and R203K-G204R in nucleocapsid have a frequency of 83% and 28% respectively in sequences from South America. ConclusionNon-synonymous substitutions were found in the spike and nucleocapsid proteins in Colombian genomes, the most frequent being D614G in Spike and R203K-G204R in nucleocapsid. These substitutions are frequent in the genomes reported for other South American countries. It is necessary to continue with genomic surveillance of the changes in Spike and Nucleocapsid proteins during the SARS-CoV-2 pandemic in Colombia and South America, even more considering that these proteins are the most commonly used antigen in serological tests. HighlightsO_LIThe spike and nucleocapsid proteins of SARS-CoV-2 circulating in Colombia and South-American countries have similar patterns of non-synonymous substitutions C_LIO_LISubstitutions D614G in Spike and R203K-G204R in Nucleocapsid are the most frequent in Colombia and South-American countries C_LI

The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main inhouse methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3' end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP and N genes were observed. The 3 end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants. HIGHLIGHTSO_LIColombian SARS-CoV-2 sequences displayed genetic variability in some target regions used for COVID-19 diagnosis. C_LIO_LIMismatches in critical primer regions could impact their performance and the rate of false negative results. C_LI

In this work, we evaluated the levels of genetic diversity in 95 genomes of the carriers of the Omicron B.1.1.529 mutation in SARS-CoV-2 from South Africa, Asia, Massachusetts-USA, Rhode Island-USA, United Kingdom and Germany. All with 29,996pb extension and recovered from GENBANK and publicly available at the National Center for Biotechnology and Information (NCBI). All gaps and conserved sites were extracted for the construction of a phylogenetic tree and for specific methodologies of estimates of paired FST, Molecular Variance (AMOVA), Genetic Distance, Incompatibility, demographic expansion analyses, molecular diversity and of evolutionary divergence time analyses, always with 20,000 random permutations. The results revealed the presence of only 75 parsimony-informative sites, sites among the 29,996bp analyzed. The analyses based on FST values, confirmed the absence of distinct genetic structuring with fixation index of 98% and with a greater component of population variation (6%) for a "p" 0.05. Tau variations (related to the ancestry of the groups), did not reveal significant moments of divergence, supported by the incompatible analysis of the observed distribution ({tau} = 0%). It is safe to say that the large number of existing polymorphisms reflects major changes in the protein products of viral populations in all countries and especially In South Africa. This consideration provides the safety that, because there are large differences between the haplotypes studied, these differences are minimal within the populations analyzed geographically and, therefore, it does not seem safe to extrapolate the results of polymorphism and molecular diversity levels found in the Variant Omicron B.1.529 of SARS-CoV-2 for wild genomes or other mutants. This warns us that, due to their higher transmission speed and infection, possible problems of molecular adjustments in vaccines already in use may be necessary in the near future.

Intra-subtype recombination is a common phenomenon among HIV strains which involves transfer of genetic information between two viral strains belonging to the same HIV subtype. However, more research has been done on inter-subtype recombination which is the transfer of genetic information between two strains belonging to different HIV subtypes. In this study HIV 1 subtype C env sequences from Zimbabwean nucleotide sequences (n=2 915) downloaded from Los Alamos HIV databases were used to investigate intra-subtype recombination. Using the GENECUTTER tool, [~]44.4% of whole genomes were selected to have informative env regions (n = 1 295). Clustal was used for Multiple Sequence Alignment and RDP 4 was used for analysis and detection of Intra-subtype recombination. Apparently, GENECONV included in RDP 4 detected 47 recombination events. One of the most informative recombination events was further analysed using UPGMA phylogenetic tree to understand the extent of the intra-subtype recombination.

Mutations primarily in the Spike (S) gene resulted in the emergence of many SARS-CoV-2 variants like Alpha, Beta, Delta and Omicron variants. This has also caused a number of COVID-19 pandemic waves which have impacted human lives in different ways due to restriction measures put in place to curb the spread of the virus. In this study, evolutionary patterns found in SARS-CoV-2 sequences of samples collected from Zimbabwean COVID-19 patients were investigated. High coverage SARS-CoV-2 whole genome sequences were downloaded from the GISAID database along with the GISAID S gene reference sequence. Biopython, NumPy and Pandas Data Science packages were used to load, slice and clean whole genome sequences outputting a fasta file with approximate Spike (S) gene sequences. Alignment of sliced dataset with GISAID reference sequence was done using Jalview 2.11.1.3 to find exact sequences of SARS-CoV-2 S gene. Evidence of recombination signals was investigated using RDP 4.1 and pervasive selection in the S gene was investigated using FUBAR algorithm hosted on the Datamonkey webserver. Matplotlib and Seaborn Python packages were used for Data Visualisation. A plot of Bayes factor hypothesizing non-synonymous substitution being greater than synonymous substitution ({beta} > ) in the S protein sites showed 3 peaks with evidence of strong divergence. These 3 diverging S protein sites were found to be D142G, D614G and P681R. No evidence of recombination was detected by 9 methods of RDP which use different approaches to detect recombination signals. This study is useful in guiding drug, vaccine and diagnostic innovations toward better control of the pandemic. Additionally, this study can guide other non-biological interventions as we better understand the changes in various viral characteristics driven by the observed evolutionary patterns.

In this work, we evaluated the levels of genetic diversity in 38 complete genomes of SARS-CoV-2 from five Central American countries (Belize, Guatemala, Cuba, Jamaica and Puerto Rico) with 04, 10, 2, 8 and 14 haplotypes, respectively, with an extension of up to 29,885 bp. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform. Using specific methodologies for paired FST, AMOVA, mismatch, demographic-spatial expansion, molecular diversity and for the time of evolutionary divergence, it was possible to notice that only 79 sites remained conserved and that the high number of polymorphisms found helped to establish a clear pattern of genetic non-structuring, based on the time of divergence between the groups. The analyses also showed that significant evolutionary divergences within and between the five countries corroborate the fact that possible rapid and silent mutations are responsible for the increase in genetic variability of the Virus, a fact that would hinder the work with molecular targets for vaccines and medications in general.

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.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has been mutating and thus variants emerged. This suggests that SARS-CoV-2 could mutate at an unsteady pace. Supportive evidence comes from the accelerated evolution which was revealed by tracking mutation rates of the genomic location of Spike protein. This process is sponsored by a small portion of the virus population but not the largest viral clades. Moreover, it generally took one to six months for current variants that caused peaks of COVID-19 cases and deaths to survive selection pressure. Based on this statistic result and the above speedy Spike evolution, another upcoming peak would come around July 2021 and disastrously attack Africa, Asia, Europe, and North America. This is the prediction generated by a mathematical model on evolutionary spread. The reliability of this model and future trends out of it comes from the comprehensive consideration of factors mainly including mutation rate, selection course, and spreading speed. Notably, if the prophecy is true, then the new wave will be the first determined by accelerated Spike evolution.

We scrutinize the evolution of Covid-19 in Madagascar by comparing results from three approaches (cubic polynomial, semi-gaussian and gaussian-like models) which we use to provide an analytical form of the spread of the pandemic. In so doing, we introduce (for the first time) the ratio [Formula] of the cumulative and daily numbers of infected persons over the corresponding one of tests which are expected to be less sensitive to the number of the tests because the credibility of the results based only on the absolute numbers often raises some criticisms. We also give and compare the reproduction number Reff from different approaches and with the ones with the ones of some European countries with a small number of population (Greece, Switzerland) and some other African countries. Finally, we show and comment the evolution of the total number of deaths and of the per cent number of cured persons and discuss the performance of the medical care.

The circulation of SARS-CoV-2 in Italy has been dominated by two large clusters of outbreaks in Northern part of the peninsula, source of alarming and prolonged infections in Lombardy region, in Codogno and Bergamo areas especially. The aim of the study was to expand understanding on the circulation of SARS-CoV-2 in the affected Lombardy areas. To this purpose, twenty full length genomes were collected from patients addressing to several Lombard hospitals from February 20th to April 4th, 2020. The obtained genome assemblies, available on the GISAD database and performed at the Referral Center for COVID-19 diagnosis, identified 2 main monophyletic clades, containing 9 and 52 isolates, respectively. The molecular clock analysis estimated a clusters divergence approximately one month before the first patient identification, supporting the hypothesis that different SARS-CoV-2 strains spread all over the world at different time, but their presence became evident only in late February along with Italian epidemic emergence. Therefore, the epidemiological reconstruction carried out by this work highlights multiple inputs of the virus into its initial circulation in Lombardy Region. However, a phylogenetic reconstruction robustness will be improved when other genomic sequences will be available, in order to guarantee a complete epidemiological surveillance.

A simplified model applied to COVID-19 cases detected and officially published by the italian government [1], seems to fit quite well the time evolution of the disease in Italy during the period feb-24th - may-19th 2020. The hypothesis behind the model is based on the fact that in the lockdown period the infection cannot be transmitted due to social isolation and, more generally, due to the strong protection measures in place during the observation period. In this case a compartment model is used and the interactions between the different compartments are simplified. The sample of cases detected is intended as a set of individuals susceptible to infection which, after being exposed and undergoing the infection, were isolated ( treated) in such a way they can no longer spread the infection. The values obtained are to be considered indicative. The same model has been applied both to the data relating to Italy and to some regions of Italy (Lombardia, Piemonte, Lazio, Campania, Calabria, Sicilia, Sardegna), generally finding a good response and indicatively interesting values (see chap. 5). The only tuning parameter is the incubation period{tau} that, together with the calculated growth rate{kappa} of the exponential curve used to approximate the early stage data, in this modelization, are in strong relationship with the compartments transfer rates. In particular[R] 0 and the numerical value of{kappa} (dimensionless) in this model are linked by the relation:[R] 0 = 1/{kappa}2 Revision HistoryO_ST_ABSRevision # 1C_ST_ABSO_LIErrata corrige in section 1 (Introduction): the equations that summarize the relationship between the parameters were wrong. This revised version contains the correct equations at page 2. C_LIO_LIThe synchronization criteria is updated. No need to use a threshold different to the one used to determine the growth coefficient. The results are now updated with the synchronization point near to the 20% of the maximum value of the cases detected per day: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD C_LIO_LIModifications in section 4 (Model results for Italy). It is appropriate to use an exponential function instead of a logistic function to find the growth rate in the initial phase. Section 4 and the results are now updated. C_LIO_LISome non-substantial corrections in the descriptive part. C_LI Revision # 2O_LIErrata corrige in the system differential equation 6: in the the derivative of S were reported a wrong additional term N. Now the equation 6 is correct. C_LI

The responsible estimation of parameters is a main issue of mathematical pandemic models. Especially a good choice of {beta} as the number of others that one infected person encounters per unit time (per day) influences the adequateness of the results of the model. For the example of the actual COVID-19 pandemic some aspects of the parameter choice will be discussed. Because of the incompatibility of the data of the Johns-Hopkins-University [3] to the data of the German Robert-Koch-Institut we use the COVID-19 data of the European Centre for Disease Prevention and Control [2] (ECDC) as a base for the parameter estimation. Two different mathematical methods for the data analysis will be discussed in this paper and possible sources of trouble will be shown. Parameters for several countries like UK, USA, Italy, Spain, Germany and China will be estimated and used in W. O. Kermack and A. G. McKendricks SIR model[1]. Strategies for the commencing and ending of social and economic shutdown measures are discussed. The numerical solution of the ordinary differential equation system of the modified SIR model is being done with a Runge-Kutta integration method of fourth order [4]. At the end the applicability of the SIR model could be shown. Suggestions about appropriate points in time at which to commence with lockdown measures based on the acceleration rate of infections conclude the paper. This paper is an improved sequel of [5].

We demonstrate that universal scaling behavior is observed in the current coronavirus (SARS-CoV-2) spread, the COVID-19 pandemic, in various countries. We analyze the numbers of infected people who tested positive (cases) in selected eleven countries (Japan, USA, Russia, Brazil, China, Italy, Indonesia, Spain, South Korea, UK, and Sweden). By using the double exponential function called the Gompertz function, fG(x) = exp(-e-x), the number of cases is well described as N(t) = N0fG({gamma}(t - t0)), where N0, 7 and t0 are the final number of cases, the damping rate of the infection probability and the peak time of the daily number of new cases, dN(t)/dt, respectively. The scaled data of cases in most of the analyzed countries are found to collapse onto a common scaling function fG(x) with x = {gamma}(t - t0) being the scaling variable in the range of fG(x) {+/-} 0.05. The recently proposed indicator so-called the K value, the increasing rate of cases in one week, is also found to show universal behavior. The mechanism for the Gompertz function to appear is discussed from the time dependence of the produced pion numbers in nucleus-nucleus collisions, which is also found to be described by the Gompertz function.

SARS-CoV-2, the etiological agent of COVID-19, was first described in Wuhan, China in December 2019 and has now spread globally. Ecuador was the second country in South America to confirm cases and Guayaquil was one of the first cities in the world to experience high mortality due to COVID-19. The aim of this study was to describe the lineages circulating throughout the country and to compare the mutations in local variants, to the reference strain. In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the whole SARS-CoV-2 genomes of 119 patients from all provinces of Ecuador, using the ARTIC network protocols. Our data from lineage assignment of the one hundred and nineteen whole genomes revealed twenty different lineages. All genomes presented differences in the S gene compared to the Wuhan reference strain, being the D614G amino acid replacement the most common change. The B.1.1.119 lineage was the most frequent and was found in several locations in the Coast and Andean region. Three sequences were assigned to the new B.1.1.7 lineage. Our work is an important contribution to the understanding of the epidemiology of SARS-CoV-2 in Ecuador and South America. HighlightsO_LIAll 119 genomes showed mutations compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. C_LIO_LIUntil January 17, three sequences were assigned to the new B.1.1.7 lineage. C_LIO_LIOur findings suggest that there were at least twenty independent introductions of SARS-CoV-2 to Ecuador. C_LI Article Summary LineWe report 119 sequences of SARS-CoV-2 across all Ecuadorian provinces, 20 different lineages were found until January 17th, including B.1.1.7.

BackgroundMolecular techniques can enhance the power of epidemiological investigations for tracing HIV transmission networks. This information could be useful for developing strategies for prevention of HIV transmission. Hence, we carried out to a study on the transmission patterns among newly diagnosed HIV cases among High-Risk Groups (HRGs) of North-West India using phylogenomic methods. MethodsPhylogenomic analysis was carried out among 37 randomly selected samples of recently infected HRGs identified through Recent Infections Testing Algorithm (RITA) using Limiting Antigen Avidity Assay. Amplification of the reverse transcriptase region of pol gene (540 base pairs) and sequencing was done. Reference sequences were extracted from HIV Los Alamos database. Sequences aligned by Clustal W and HIV-1 subtype were determined on the basis of phylogenomic analysis of the pol sequence. Phylogenetic trees were constructed using the MEGA (version 11.0). ResultsThe phylogeny clearly depicts that the study isolates RTFSWCHD and RTFSWPB007 cluster with and are related to the Indian reference sequences AY746371 and EU683781 and a Nepalese sequence KX430115.The other study isolates (RTFSWCHD001, RTFSWPB005, RTFSWCHD002, RTFSWPB006, RTFSWHR008, RTFSWHR 009) clustered uniquely among themselves without any interlinking with other references. One study isolate (RTFSWHP004) clustered closely with Zimbabwian isolate AY998351. The phylogeny shows that the study isolate MSMCHD005 clades separately with the Indian references (DQ838761, EU683781and AY746371), but is also very closely related to the references from China (HG421606, JQ658754), Nepal(JN023039) and Myanmar (N223216, JN223183, KC913773). Other study isolates (MSMCHD003, MSMHP007, MSMCHD004, MSMPB001, MSMPB002, and MSMHR006) are highly interrelated among themselves and form a separate unique clade together. The evolutionary tree shows that all the sequences from current study formed a monophyletic lineage, i.e., sequences from India clustered together more than with sequences from any other country. The study sequences showed relatedness only to the Nepal references KX430115 and JN023035. The South African, UK, Norway, China, and Myanmar references are grouped into aseparate clade. ConclusionMolecular epidemiologic methods were able to reveal transmission networks; hence, phylogenomic methods can be used in HIV Sentinel Surveillance to monitor transmission networks.

Delta VOC is highly diverse and more than 120 sublineages have been identified in Pango lineages with the continuous description of emerging ones. Brazil is now one of the most vaccinated countries against SARS-CoV-2 in the world which can enhance the emergence of viral mutations related to improved viral fitness. In this study, we identified two novel sublineages of the AY.43 lineage which were classified as AY.43.1 and AY.43.2 as observed on the specific clustering on the obtained phylogenetic tree. The novel sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages were Brazilian, which shows that probably these two emerging sublineages have Brazilian origin. It is still unknown how these two sublineages are disseminated in Sao Paulo State and Brazil and their potential impact on the ongoing vaccination process. However, the performed study reinforces the importance of the SARS-CoV-2 genome monitoring for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.

The COVID-19 pandemic in Brazil has demonstrated an important public health impact, as has been observed in the world. In Brazil, the Amazon Region contributed with a large number of cases of COVID-19, especially in the beginning of the circulation of SARS-CoV-2 in the country. Thus, we describe the epidemiological profile of COVID-19 and the genetic diversity of SARS-CoV-2 strains circulating in the Amazon Region. We observe an extensive spread of virus in this Brazilian site. The data on sex, age and symptoms presented by the investigated individuals were similar to what has been observed worldwide. The genomic analysis of the viruses revealed important amino acid changes, including the D614G and the I33T in Spike and ORF6 proteins, respectively. The latter found in strains originating in Brazil. The phylogenetic analyzes demonstrated the circulation of the lineages B.1 and B.1.1, whose circulation in Brazil has already been previous reported. Our data reveals molecular epidemiology of SARS-CoV-2 in the Amazon Region. These findings also reinforce the importance of continuous genomic surveillance this virus with the aim of providing accurate and updated data to understand and map the transmission network of this agent in order to subsidize operational decisions in public health.

In this work the Luria and Delbruck Fluctuation Test was applied to the data of Morbidity and Mortality by COVID-19 in China from January 2020 to August 2023. Three types of data were used: es.statista.com, datosmacro.expansion.com and larepublica.co without modification, but trying to avoid and justify the anomalies and inconsistencies observed. The methods originally used to establish the interactions of two populations were evaluated: the viral population with that of its host and the drift of both organisms. Only the fluctuations of the weekly Variance of daily increase of Cases (Morbidity) and of the weekly Variance of daily increase of Deaths (Mortality) were studied. The results showed that the Fluctuation Test is applicable to the selected data from China and other data from India, Japan and South Korea, used as controls. The study was separated into two periods: a first initial period from January 2020 to September 2021 and a second final period from October 2021 to August 2023. Results were obtained for Morbidity and Mortality that relate the fluctuations of the first with the fluctuations of the second. However, it was possible to detect some anomalies and uncertainties that were possibly derived from inconsistencies in the original data. A repeated fluctuation was observed in the boreal winter in January, February and March of each one of the year studied. A clear decrease in fluctuation was detected in that period in 2021 that could be attributed to the strict confinement during the quarantine in China between 2020 and 2021. Massive, extensive and intensive vaccinations failed to completely eliminate the most important fluctuations. In this work we tried to correlate the appearance of some virus variants with the fluctuations. The most relevant results of said correlation are presented. With the results of this work, the animal origin cannot be confirmed nor can the human or laboratory origin of the SARS CoV-2 virus that caused the initial emerging infection, be ruled out. However, it was concluded that this method could be used to search for clues about its origin. One of these keys is the comparison of the result of the first important fluctuation in the boreal winter of 2020 in each of the countries studied as controls: India, Japan and South Korea. The comparison of this result with the first fluctuation of China for that same period could give clues about the origin of the virus.

BackgroundThe genetic diversity of persistent infectious agents, such as HHV-8, correlates closely with the migration of modern humans out of East Africa which makes them useful to trace human migrations. However, there is scarce data about the evolutionary history of HHV-8 particularly in multiethnic Latin American populations. ObjectivesThe aim of this study was to characterize the genetic diversity and the phylogeography of HHV-8 in two distant geographic regions of Argentina and to establish potential associations with the genetic ancestry of the population. Study designA total of 605 HIV-1 infected subjects, Kaposis Sarcoma (KS) patients and blood donors were recruited in the metropolitan (MET) and north-western regions of Argentina (NWA). After HHV-8 DNA detection, ORF-26 and ORF-K1 were analyzed for subtype assignment. Uniparental and biparental ancestry markers were evaluated in samples in which subtypes could be assigned. Phylogeographic analysis was performed in the ORF-K1 sequences from this study combined with 388 GenBank sequences. ResultsHHV-8 was detected in 24.8% of samples. ORF-K1 phylogenetic analyses showed that subtypes A (A1-A5), B1, C (C1-C3) and F were present in 46.9%, 6.25%, 43.75% and 3.1% of cases, respectively. Analyses of ORF-26 fragment revealed that 81.95% of strains were subtypes A/C followed by J, B2, R, and K. Among KS patients, subtype A/C was more commonly detected in MET whereas subtype J was the most frequent in NWA. Subtypes A/C was significantly associated with Native American maternal haplogroups (p=0.004), whereas subtype J was related to non-Native American haplogroups (p<0.0001). Sub-Saharan Africa, Europe and Latin America were the most probable locations from where HHV-8 was introduced to Argentina. ConclusionsThese results give evidence of the geographic circulation of HHV-8 in Argentina, provide new insights about its relationship with ancient and modern human migrations and identify the possible origins of this virus in Argentina.

In this work the Luria and Delbruck Fluctuation Test was comparatively applied to the data of Morbidity by COVID-19 in the United States of America (USA), United Kingdom (UK), Taiwan and China from 2020 to 2023. Three types of data were used: es.statista.com, datosmacro.expansion.com and larepublica.co without modification, but trying to avoid and justify the anomalies and inconsistencies observed. The methods originally used to establish the interactions of two populations were evaluated: the viral population with that of its host and the drift of both organisms. Only the interactive fluctuations of the weekly Variance of daily increase of Cases (Morbidity) were studied. The results showed that the Fluctuation Test is applicable to the selected data from USA, UK, Taiwan and China and other data from several countries used as controls. The study was separated into two approaches: First, comparison of the total or partial logarithmic profile of fluctuations of Variance of Cases (Morbidity) of USA, UK, Taiwan and China. Second, comparison of the values of the first fluctuation of Variance of Cases (Morbidity) in the boreal winter of 2020 for USA, UK, Taiwan, China and several countries used as controls. The results obtained for Morbidity demonstrate that USA and UK present a similar bimodal profile. China shows an inverted profile and Taiwan shows an intermediate profile between both tendencies. However, it was possible to detect some anomalies and uncertainties that were possibly derived from inconsistencies in the original data. Only USA shows a value of the first fluctuation comparable to the order of magnitude of the value of the first fluctuation of the Variance of Cases of China, in the northern winter of 2020. In the First Approach USA, UK and China had two important fluctuations: the first in the northern winter of 2020 before week 16 and the second at the beginning of northern winter of 2022, more than 100 weeks later. Taiwan showed only the latter. This latest fluctuation coincides with two events: the possible achievement of herd immunity and the emergence of Omicron variant. In this work we have evaluated whether this coincidence is casual or causal. The results obtained in the Second Approach aim to confirm the hypothesis of the animal origin of the first variant of SARS CoV-2.