The Lambda Variant in Argentina: Analyzing the Evolution and Spread of SARS-CoV-2 Lineage C.37.

The second wave of COVID-19 occurred in South America in early 2021 and was mainly driven by Gamma and Lambda variants. In this study, we aimed to describe the emergence and local genomic diversity of the SARS-CoV-2 Lambda variant in Argentina, from its initial entry into the country until its detection ceased. Molecular surveillance was conducted on 9356 samples from Argentina between October 2020 and April 2022, and sequencing, phylogenetic, and phylogeographic analyses were performed. Our findings revealed that the Lambda variant was first detected in Argentina in January 2021 and steadily increased in frequency until it peaked in April 2021, with continued detection throughout the year. Phylodynamic analyses showed that at least 18 introductions of the Lambda variant into the country occurred, with nine of them having evidence of onward local transmission. The spatial--temporal reconstruction showed that Argentine clades were associated with Lambda sequences from Latin America and suggested an initial diversification in the Metropolitan Area of Buenos Aires before spreading to other regions in Argentina. Genetic analyses of genome sequences allowed us to describe the mutational patterns of the Argentine Lambda sequences and detect the emergence of rare mutations in an immunocompromised patient. Our study highlights the importance of genomic surveillance in identifying the introduction and geographical distribution of the SARS-CoV-2 Lambda variant, as well as in monitoring the emergence of mutations that could be involved in the evolutionary leaps that characterize variants of concern.

Omicron Waves in Argentina: Dynamics of SARS-CoV-2 Lineages BA.1, BA.2 and the Emerging BA.2.12.1 and BA.4/BA.5.

The COVID-19 pandemic has lately been driven by Omicron. This work aimed to study the dynamics of SARS-CoV-2 Omicron lineages during the third and fourth waves of COVID-19 in Argentina. Molecular surveillance was performed on 3431 samples from Argentina, between EW44/2021 and EW31/2022. Sequencing, phylogenetic and phylodynamic analyses were performed. A differential dynamic between the Omicron waves was found. The third wave was associated with lineage BA.1, characterized by a high number of cases, very fast displacement of Delta, doubling times of 3.3 days and a low level of lineage diversity and clustering. In contrast, the fourth wave was longer but associated with a lower number of cases, initially caused by BA.2, and later by BA.4/BA.5, with doubling times of about 10 days. Several BA.2 and BA.4/BA.5 sublineages and introductions were detected, although very few clusters with a constrained geographical distribution were observed, suggesting limited transmission chains. The differential dynamic could be due to waning immunity and an increase in population gatherings in the BA.1 wave, and a boosted population (for vaccination or recent prior immunity for BA.1 infection) in the wave caused by BA2/BA.4/BA.5, which may have limited the establishment of the new lineages.

Assessing the hidden diversity underlying consensus sequences of SARS-CoV-2 using VICOS, a novel bioinformatic pipeline for identification of mixed viral populations.

INTRODUCTION: Coinfection with two SARS-CoV-2 viruses is still a very understudied phenomenon. Although next generation sequencing methods are very sensitive to detect heterogeneous viral populations in a sample, there is no standardized method for their characterization, so their clinical and epidemiological importance is unknown. MATERIAL AND METHODS: We developed VICOS (Viral COinfection Surveillance), a new bioinformatic algorithm for variant calling, filtering and statistical analysis to identify samples suspected of being mixed SARS-CoV-2 populations from a large dataset in the framework of a community genomic surveillance. VICOS was used to detect SARS-CoV-2 coinfections in a dataset of 1,097 complete genomes collected between March 2020 and August 2021 in Argentina. RESULTS: We detected 23 cases (2%) of SARS-CoV-2 coinfections. Detailed study of VICOS's results together with additional phylogenetic analysis revealed 3 cases of coinfections by two viruses of the same lineage, 2 cases by viruses of different genetic lineages, 13 were compatible with both coinfection and intra-host evolution, and 5 cases were likely a product of laboratory contamination. DISCUSSION: Intra-sample viral diversity provides important information to understand the transmission dynamics of SARS-CoV-2. Advanced bioinformatics tools, such as VICOS, are a necessary resource to help unveil the hidden diversity of SARS-CoV-2.

Analysis of COL7A1 pathogenic variants in a large cohort of dystrophic epidermolysis bullosa patients from Argentina reveals a new genotype-phenotype correlation.

Dystrophic epidermolysis bullosa (DEB) is a clinically heterogeneous heritable skin disorder, characterized by blistering of the skin and mucous membranes following minor trauma. Dominant (DDEB) and recessive (RDEB) forms are caused by pathogenic variants in COL7A1 gene. Argentina's population has a heterogeneous genetic background, and little is known about the molecular basis of DEB in our country or in native South American populations. In this study, we present the prevalence and geographical distribution of pathogenic variants found in 181 patients from 136 unrelated families (31 DDEB and 105 RDEB). We detected 95 different variants, 59 of them were previously reported in the literature and 36 were novel, nine of which were detected in more than one family. The most prevalent pathogenic variants were identified in exon 73 in DDEB patients and in exon 3 in RDEB patients. We also report a new phenotype-genotype correlation found in 10 unrelated families presenting mild blistering and severe mucosal involvement. Molecular studies in populations with an unexplored genetic background like ours revealed a diversity of pathogenic variants, and we hope that these findings will contribute to the definition of targets for new gene therapies.

First detection and molecular analysis of SARS-CoV-2 from a naturally infected cat from Argentina.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has rapidly spread worldwide. Studies of transmission of the virus carried out in animals have suggested that certain animals may be susceptible to infection with SARS-CoV-2. The aim of the present study was to investigate the infection of SARS-CoV-2 in pets (18 cats and 20 dogs) from owners previously confirmed as COVID-19-positive. Oropharyngeal and rectal swabs were taken and analyzed by real-time RT-PCR assays, while blood samples were taken for antibody detection. Of the total pets analyzed, one cat was found reactive to SARS-CoV-2 by real-time RT-PCR of an oropharyngeal and a rectal swab. This cat presented only sneezing as a clinical sign. Serological analysis confirmed the presence of antibodies in the serum sample from this cat, as well as in the serum from another cat non-reactive to real-time RT-PCR. Complete sequence and phylogenetic analysis allowed determining that the SARS-CoV-2 genome belonged to the B.1.499 lineage. This lineage has been reported in different provinces of Argentina, mainly in the Metropolitan Area of Buenos Aires. This study notifies the first detection of the natural infection and molecular analysis of SARS-CoV-2 in a cat from Argentina whose owner where COVID-19-positive. Although there is currently no evidence that cats can spread COVID-19, results suggest that health authorities should test pets with COVID-19-positive owners.

Ichthyosis follicularis, atrichia and photophobia (IFAP) and hereditary mucoepithelial dysplasia: Two syndromes that share a common clinical spectrum.

Ichthyosis follicularis, atrichia and photophobia syndrome (IFAP) is an X-linked inherited disease caused by pathogenic variants in the gene encoding the membrane-bound transcription factor peptidase, site 2 (MBTPS2). Clinical presentation includes ichthyosis follicularis, alopecia, photophobia and developmental delay. Hereditary mucoepithelial dysplasia (HMD) is a dominantly inherited disease characterized by keratitis, non-scarring alopecia, skin lesions including follicular keratosis, perineal erythema, and mucosal involvement. Recently, variants in SREBF1, a gene coding for a transcription factor related to cholesterol and fatty acid synthesis, have been associated with the disease. These two syndromes share a common clinical spectrum. Here, we describe an IFAP syndrome patient with a novel variant in the MBTPS2 gene and an HMD patient with a previously reported variant in the SREBF1 gene. In addition, we present a review of the literature describing the triad characterized by non-scarring alopecia, keratosis follicularis, and ocular symptoms common in both IFAP and HMD patients to raise awareness of these underdiagnosed diseases. We also highlight the subtle differences in clinical presentation between the two disorders to better enable differentiation.

Circulation of human coronaviruses OC43 and 229E in Córdoba, Argentina.

This is the first study of respiratory infections in Córdoba, Argentina, caused by endemic human coronavirus (HCoV)-OC43 and HCOV-229E, which circulated during 2011-2012 at a 3% rate, either as single or multiple infections. They were detected mainly in children, but HCoV-229E was also found in adults. HCoV-229E was detected in five out of 631 samples (0.8%), and HCoV-OC43 was found in 14 out of 631 (2.2%) samples. Clinical manifestations ranged from fever to respiratory distress, and a significant association of HCoV-229E with asthma was observed. Further studies and surveillance are needed to provide better clinical insights, early diagnosis, and medical care of patients, as well as to contribute to epidemiology modeling and prevention.

Genotipificación del virus de la enfermedad mano-pie-boca atípica en un hospital pediátrico de la Ciudad de Buenos Aires, Argentina / Atypical hand-foot-mouth disease virus genotyping in a pediatric hospital in Buenos Aires city, Argentin

La enfermedad mano-pie-boca (EMPB) típica es exantemática, con sintomatología clásica de fiebre, exantema papulovesicular en las manos y los pies, asociada o no a herpangina. Es causada, principalmente, por enterovirus 71 y virus Coxsackie A16, miembros del género Enterovirus. En los últimos años, se han descrito brotes mundiales de EMPB con manifestaciones atípicas causadas, sobre todo, por el virus Coxsackie A6. La EMPB atípica se considera emergente con características clínicas y epidemiológicas peculiares: la afección de adultos, el predominio en invierno y un amplio espectro de manifestaciones clínicas en la extensión y la distribución de las lesiones. Las características morfológicas de las lesiones son muy variables: pueden simular varicela, impétigo o vasculitis.Se describe el caso de un niño de 4 años con EMPB atípica. Se detalla su forma de presentación, evolución clínica, metodología diagnóstica y terapéutica empleada.

Typical hand-foot-mouth disease (HFMD) is an exanthematous viral disease with a classic symptomatology of fever, papulovesicular rash on the hands and feet with or without herpangina. It is usually caused by enterovirus 71 and Coxsackievirus A16, members of the genus Enterovirus. Recently, worldwide outbreaks of HFMD with atypical manifestations caused by Coxsackievirus A6 have been described. Atypical HFMD is considered an emerging disease due to its peculiar clinical and epidemiological characteristics: it affects adults, has a wide spectrum of clinical manifestations in the extension and distribution of the lesions and occurs in winter. The morphological characteristics of the lesions are very variable and can be misdiagnosed as chickenpox, impetigo or vasculitis. Here we describe the symptoms, clinical evolution, diagnostic methodology and treatment employed on a 4-year-old male patient with atypical HFMD.

[Atypical hand-foot-mouth disease virus genotyping in a pediatric hospital in Buenos Aires city, Argentina]. / Genotipificación del virus de la enfermedad mano-pie-boca atípica en un hospital pediátrico de la Ciudad de Buenos Aires, Argentina.

Typical hand-foot-mouth disease (HFMD) is an exanthematous viral disease with a classic symptomatology of fever, papulovesicular rash on the hands and feet with or without herpangina. It is usually caused by enterovirus 71 and Coxsackievirus A16, members of the genus Enterovirus. Recently, worldwide outbreaks of HFMD with atypical manifestations caused by Coxsackievirus A6 have been described. Atypical HFMD is considered an emerging disease due to its peculiar clinical and epidemiological characteristics: it affects adults, has a wide spectrum of clinical manifestations in the extension and distribution of the lesions and occurs in winter. The morphological characteristics of the lesions are very variable and can be misdiagnosed as chickenpox, impetigo or vasculitis. Here we describe the symptoms, clinical evolution, diagnostic methodology and treatment employed on a 4-yearold male patient with atypical HFMD.

La enfermedad mano-pie-boca (EMPB) típica es exantemática, con sintomatología clásica de fiebre, exantema papulovesicular en las manos y los pies, asociada o no a herpangina. Es causada, principalmente, por enterovirus 71 y virus Coxsackie A16, miembros del género Enterovirus. En los últimos años, se han descrito brotes mundiales de EMPB con manifestaciones atípicas causadas, sobre todo, por el virus Coxsackie A6. La EMPB atípica se considera emergente con características clínicas y epidemiológicas peculiares: la afección de adultos, el predominio en invierno y un amplio espectro de manifestaciones clínicas en la extensión y la distribución de las lesiones. Las características morfológicas de las lesiones son muy variables: pueden simular varicela, impétigo o vasculitis. Se describe el caso de un niño de 4 años con EMPB atípica. Se detalla su forma de presentación, evolución clínica, metodología diagnóstica y terapéutica empleada.

A novel pathogenic FERMT1 variant in four families with Kindler syndrome in Argentina.

BACKGROUND: Kindler syndrome is a rare genodermatosis. Major clinical criteria include acral blistering in infancy and childhood, progressive poikiloderma, skin atrophy, abnormal photosensitivity, and gingival fragility. METHODS: FERMT1 gene was sequenced in 5 patients with a clinical diagnosis of Kindler syndrome. RESULTS: We report a novel pathogenic variant detected in four unrelated families of Paraguayan origin, where one nucleotide deletion in FERMT1 gene (c.450delG) is predicted to cause a frameshift mutation leading to loss of function. Haplotype analysis revealed the propagation of an ancestral allele through this population. CONCLUSIONS: The identification of this recurrent pathogenic variant enables optimization of molecular detection strategies in our patients, reducing the cost of diagnosis.

An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates.

Over the last decade, the number of viral genome sequences deposited in available databases has grown exponentially. However, sequencing methodology vary widely and many published works have relied on viral enrichment by viral culture or nucleic acid amplification with specific primers rather than through unbiased techniques such as metagenomics. The genome of RNA viruses is highly variable and these enrichment methodologies may be difficult to achieve or may bias the results. In order to obtain genomic sequences of human respiratory syncytial virus (HRSV) from positive nasopharyngeal aspirates diverse methodologies were evaluated and compared. A total of 29 nearly complete and complete viral genomes were obtained. The best performance was achieved with a DNase I treatment to the RNA directly extracted from the nasopharyngeal aspirate (NPA), sequence-independent single-primer amplification (SISPA) and library preparation performed with Nextera XT DNA Library Prep Kit with manual normalization. An average of 633,789 and 1,674,845 filtered reads per library were obtained with MiSeq and NextSeq 500 platforms, respectively. The higher output of NextSeq 500 was accompanied by the increasing of duplicated reads percentage generated during SISPA (from an average of 1.5% duplicated viral reads in MiSeq to an average of 74% in NextSeq 500). HRSV genome recovery was not affected by the presence or absence of duplicated reads but the computational demand during the analysis was increased. Considering that only samples with viral load ≥ E+06 copies/ml NPA were tested, no correlation between sample viral loads and number of total filtered reads was observed, nor with the mapped viral reads. The HRSV genomes showed a mean coverage of 98.46% with the best methodology. In addition, genomes of human metapneumovirus (HMPV), human rhinovirus (HRV) and human parainfluenza virus types 1-3 (HPIV1-3) were also obtained with the selected optimal methodology.

Diagnóstico molecular de paquioniquia congénita / Molecular diagnosis of congenital pachyonychia

La paquioniquia congenital (PC) es una genodermatosis poco frecuente, caracterizada por presentar queratodermia palmoplantar dolorosa y debilitante, uñas hipertróficas, hiperqueratosis folicular, quistes epidérmicos, leucoqueratosis oral y ocasionalmente hiperhidrosis, ronquera y dientes natales. Está asociada a mutaciones heterocigotas en los genes que codifican queratinas 6a, 6b, 6c, 16 y 17. Se presenta una familia con dos miembros en dos generaciones afectados por PC: un niño de 2 años de edad con alteración de la coloración, hiperqueratosis de las 20 uñas, con dolor periungueal, múltiples pápulas foliculares color piel en tronco y dientes natales y su madre, con alteración del esmalte dentario, distrofia hipertrófica de las 20 uñas, cromoniquia, queratodermia plantar dolorosa y múltiples esteatocistomas de distribución generalizada.En ambos, se realizó el diagnóstico molecular por secuenciación masiva de exoma clínico, el cual confirmó el diagnóstico clínico y permitió determinar inequívocamente el tipo de PC en el niño, motivo de ésta presentación.

Pachyonychia congenital (PC) is a rare genodermatosis characterized by painful palmoplantar keratoderma, hypertrophic nail dystrophy, follicular hyperkeratosis, epidermal cysts, oral leukokeratosis and, less commonly, palmoplantar hyperhidrosis, hoarseness and natal teeth. PC is caused by mutations in keratin 6a, 6b, 6c, 16 and 17 genes. We report a family with two members in two generations affected by PC: a two-year old boy, presenting abnormal pigmentation and hyperkeratosis of the 20 nails, perionychium pain, multiple skin-colored follicular papules on the trunk and natal teeth. His mother has dental enamel defects, hypertrophic dystrophy of the fingernails and toenails, chromonychia, painful plantar keratoderma and generalized steatocystoma multiplex. We performed the molecular diagnosis by clinical exome massive sequencing which allowed us to confirm the clinical diagnosis and to determine the specific type of PC in our patient.

Dengue Virus 1 Outbreak in Buenos Aires, Argentina, 2016.

The largest outbreak of dengue in Buenos Aires, Argentina, occurred during 2016. Phylogenetic, phylodynamic, and phylogeographic analyses of 82 samples from dengue patients revealed co-circulation of 2 genotype V dengue virus lineages, suggesting that this virus has become endemic to the Buenos Aires metropolitan area.

Molecular evidence of St. Louis encephalitis virus infection in patients in Buenos Aires, Argentina.

We report two cases of St. Louis encephalitis where the virus was detected in patients' sera directly by molecular techniques allowing subsequent typing. Phylogenetic analysis of both samples showed that NS5 sequences clustered with viruses previously classified as genotype III.

Emergence of intratreatment resistance to oseltamivir in pandemic influenza A H1N1 2009 virus.

BACKGROUND: Pandemic influenza A H1N1 2009 virus presents a new challenge to health authorities and communities worldwide. In Argentina, the outbreak was at its peak by the end of June 2009, during the southern winter. A systematic analysis of samples from patients with pandemic H1N1 2009 studied in our laboratory (Virology Laboratory, Hospital de Niños R Gutiérrez, Buenos Aires, Argentina) detected two patients presenting intratreatment emergence of the H275Y neuraminidase mutation, which confers resistance to oseltamivir. METHODS: Complementary DNAs, including the 275 codon, were obtained by reverse transcriptase PCR using viral RNAs extracted from nasopharyngeal or tracheal aspirates. Conventional sequencing and pyrosequencing were performed on each sample. In order to measure the virus susceptibility to oseltamivir, 50% inhibitory concentration determinations were performed by chemiluminescence. RESULTS: Sequential samples of two paediatric patients under oseltamivir treatment were analysed. Pretreatment samples were composed of 100% oseltamivir-sensitive variants. In case 1, the oseltamivir-resistant variant was found 8 days after the beginning of treatment. In case 2, the viral population became resistant on the second day of treatment, with 83% of the viral population bearing the mutation and this reached 100% on the seventh day. CONCLUSIONS: We describe the intratreatment emergence of oseltamivir resistance in two paediatric patients. Pyrosequencing allowed us to detect variant mixtures, showing the transition of the viral population from sensitive to resistant.

Phylogenetic analysis of rubella viruses isolated in 2008 outbreak in Argentina.

BACKGROUND: A rubella outbreak was recorded in Buenos Aires during 2008. OBJECTIVES: The objective of this communication is to present the genetic and phylogenetic analyses of wild-type RUBV circulating in Buenos Aires during the 2008 outbreak. STUDY DESIGN: Throat swab samples collected from patients diagnosed with rubella between June 2008 and December 2008 were inoculated in cell culture and 23 isolates were sequenced. RESULTS: Phylogenetic analysis of the WHO-recommended window (nt 8731-9469) of the E1 envelope glycoprotein was performed and all isolates clustered with the 2B genotype. CONCLUSIONS: Genotype 2B seems to be endemically circulating in the Southern cone of Latin America, thus causing recent outbreaks.

Recombinant production of human microsomal cytochrome P450 2D6 in the methylotrophic yeast Pichia pastoris.

Microsomal cytochrome P450 monooxygenases of groups 1-3 are mainly expressed in the liver and play a crucial role in phase 1 reactions of xenobiotic metabolism. The cDNAs encoding human CYP2D6 and human NADPH-P450 oxidoreductase (CPR) were transformed into the methylotrophic yeast Pichia pastoris and expressed with control of the methanol-inducible AOX1 promoter. The determined molecular weights of the recombinant CYP2D6 and CPR closely matched the calculated values of 55.8 and 76.6 kDa. CPR activity was detected by conversion of cytochrome c by using isolated microsomes. Nearly all of the recombinant CYP was composed of the active holoenzyme, as confirmed by reduced CO difference spectra, which showed a single peak at 450 nm. Only by coexpression of human CPR and CYP was CYP2D6 activity obtained. Microsomes containing human CPR and CYP2D6 converted different substrates, such as 3-cyano-7-ethoxycoumarin, parathion and dextrometorphan. The kinetic parameters of dextrometorphan conversion closely matched those of CYP2D6 from other recombinant expression systems and human microsomes. The endogenous NADPH-P450 oxidoreductase of Pichia pastoris seems to be incompatible with human CYP2D6, as expression of CYP2D6 without human CPR did not result in any CYP activity. These recombinant strains provide a novel, easy-to-handle and cheap source for the biochemical characterisation of single microsomal cytochromes, as well as their allelic variants.