Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern.

The pandemic generated by SARS-Cov-2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they may evade the protection generated by vaccination campaigns, their greater capacity to be transmitted, or their higher virulence. We analyzed the circulating variants in Peru after improving our Genomic Surveillance program. The results indicate a steep increase of the lambda lineage (C.37) until becoming predominant between January and April 2021, despite the cocirculation of other variants of concern or interest. Lambda lineage deserves close monitoring and could probably become a variant of concern in the near future.

Evaluation of Plasmodium falciparum MSP10 and its development as a serological tool for the Peruvian Amazon region.

BACKGROUND: Different antigens are needed to characterize Plasmodium falciparum infection in terms of seroreactivity and targets for invasion inhibition, in order to guide and identify the proper use of such proteins as tools for the development of serological markers and/or as vaccine candidates. METHODS: IgG responses in 84 serum samples from individuals with P. falciparum infection [classified as symptomatic (Sym) or asymptomatic (Asym)], or acute Plasmodium vivax infection, from the Peruvian Amazon region, were evaluated by enzyme-linked immunosorbent assays specific for a baculovirus-produced recombinant protein P. falciparum Merozoite Surface Protein 10 (rMSP10) and for non-EGF region selected peptides of PfMSP10 selected by a bioinformatics tool (PfMSP10-1, PfMSP10-2 and PfMSP10-3). Monoclonal antibodies against the selected peptides were evaluated by western blotting, confocal microscopy and inhibition invasion assays. RESULTS: Seroreactivity analysis of the P. falciparum Sym- and Asym-infected individuals against rMSP10 showed a higher response as compared to the individuals with P. vivax acute infection. IgG responses against peptide PfMSP10-1 were weak. Interestingly high IgG response was found against peptide PfMSP10-2 and the combination of peptides PfMSP10-1 + PfMSP10-2. Monoclonal antibodies were capable of detecting native PfMSP10 on purified schizonts by western blot and confocal microscopy. A low percentage of inhibition of merozoite invasion of erythrocytes in vitro was observed when the monoclonal antibodies were compared with the control antibody against AMA-1 antigen. Further studies are needed to evaluate the role of PfMSP10 in the merozoite invasion. CONCLUSIONS: The rMSP10 and the PfMSP10-2 peptide synthesized for this study may be useful antigens for evaluation of P. falciparum malaria exposure in Sym and Asym individuals from the Peruvian Amazon region. Moreover, these antigens can be used for further investigation of the role of this protein in other malaria-endemic areas.

Glycoprotein G (gG) production profile during infectious laryngotracheitis virus (ILTV) infection.

Glycoprotein G (gG) is a conserved protein, and it has been described as a chemokine-binding protein in most members of the alphaherpesviruses. In case of the infectious laryngotracheitis virus (ILTV), an alphaherpesvirus that infects chickens, this protein is a virulence factor that plays an immunomodulatory role in the chicken immune response. Nevertheless, the gG production profile during ILTV infection has not yet been studied. In this study, we developed monoclonal antibodies in order to determine the gG production profile during ILTV infection in chicken hepatocellular carcinoma (LMH) cell cultures as well as embryonated specific-pathogen-free (SPF) chicken eggs and SPF chickens using a sandwich enzyme-linked immunosorbent assay (ELISA). Despite the fact that inoculated LMH cell cultures showed an increase in both gG production and viral genome copy number up to 96 h after inoculation, we observed that gG production started earlier than the increase in viral genome copy number in ILTV infected embryonated SPF chicken eggs. Likewise, a gG production peak and an increase of viral genome copy number was observed prior to the appearance of clinical signs in infected SPF chickens. According to the production profiles, gG was also produced quite early in eggs and chickens inoculated with ILTV. These findings contribute to the knowledge of the gG role during the ILTV infection as a virulence factor.

Development of a lateral flow test for the rapid detection of Avibacterium paragallinarum in chickens suspected of having infectious coryza.

BACKGROUND: Infectious coryza (IC) is an acute respiratory disease of growing chickens and layers caused by Avibacterium paragallinarum. The development of tools that allow rapid pathogen detection is necessary in order to avoid disease dissemination and economic losses in poultry. An Av. paragallinarum-specific Ma-4 epitope of the TonB-dependent transporter (TBDT) was selected using bioinformatic tools in order to immunize a BalbC mouse and to produce monoclonal antibodies to be used in a lateral flow test (LFT) developed for Av. paragallinarum detection in chicken nasal mucus samples. RESULTS: The 1G7G8 monoclonal antibody was able to detect TBDT in Av. paragallinarum cultures (serogroups: A, B and C) by Western blot and indirect ELISA assay. Consequently, we developed a self-pairing prototype LFT. The limit of detection of the prototype LFT using Av. paragallinarum cultures was 1 × 104 colony-forming units (CFU)/mL. Thirty-five nasal mucus samples from chickens suspected of having infectious coryza were evaluated for the LFT detection capacity and compared with bacterial isolation (B.I) and polymerase chain reaction (PCR). Comparative indicators such as sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive values (NPV) and the kappa index (K) were obtained. The values were 100.0% Se, 50% Sp, 65.4% PPV, 100% NPV, and 0.49 K and 83.9% Se, 100% Sp, 100% PPV, 44.4% NPV, and 0.54 K for the comparison of the LFT with B.I and PCR, respectively. Additionally, the LFT allowed the detection of Av. paragallinarum from coinfection cases of Av. paragallinarum with Gallibacterium anatis. CONCLUSIONS: The results indicate that the self-pairing prototype LFT is suitable for the detection of TBDT in Av. paragallinarum cultures as well as in field samples such as nasal mucus from Av. paragallinarum-infected chickens. Therefore, this prototype LFT could be considered a rapid and promising tool to be used in farm conditions for Av. paragallinarum diagnosis.

Whole-Genome Sequence of Sphingomonas sp. Strain FARSPH, a Novel Sf9 Insect Cell Culture Contaminant.

Here, we report the whole-genome sequence of Sphingomonas sp. strain FARSPH, isolated from an insect cell line as a contaminant. FARSPH shared high identity with Sphingomonas melonis and Sphingomonas aquatilis strains. Due to this finding, we recommend taking this genus into consideration for cell culture quality control.

Full-Genome Sequence of Infectious Laryngotracheitis Virus (Gallid Alphaherpesvirus 1) Strain VFAR-043, Isolated in Peru.

We report here the first genome sequence of infectious laryngotracheitis virus isolated in Peru from tracheal tissues of layer chickens. The genome showed 99.98% identity to the J2 strain genome sequence. Single nucleotide polymorphisms were detected in five gene-coding sequences related to vaccine development, virus attachment, and viral immune evasion.

Phylogenetic Evidence of a Close Relationship between the Peruvian Strain Vfar-043 and Two U.S. Origin Iltv Field Strains.

Infectious laryngotracheitis virus (ILTV) is the causative agent of an acute respiratory avian disease known as infectious laryngotracheitis (ILT), which has been associated with economic losses in poultry. The presence of ILTV has been widely reported in South American countries; however, only one full genomic sequence (VFAR-043 strain) has been recently published, from an outbreak in Peru. The aim of this study was to determine the genetic relationship of the Peruvian strain with other ILTV strains from different geographic regions. The phylogenetic analyses revealed a close relationship between VFAR-043 and two U.S. origin strains (1874C5 and J2) using only the whole genome, Unique Long (UL), and Unique Short (US) genomic regions. Then these three genomic sequences were compared to evaluate their genetic variations using the USDAref as a reference strain. Genetic variations such as synonymous and nonsynonymous single-nucleotide polymorphisms, insertions, deletions, and nucleotide-codon variations were identified among these three strains. Moreover, the phylogenetic tree analysis using gene sequences of the US5 and ICP4 coding regions from South American isolates showed that VFAR-043 does not have a close relationship with either the Argentinian (US5) or Brazilian (ICP4) reported sequences. However, a close relationship was observed between VFAR-043 and another Peruvian isolate (USP-81) when the ICP4 gene sequence was analyzed. All these results suggest that VFAR-043 together with 1874C5 and J2 are closely related. These findings contribute to our understanding of the epidemiology of ILTV in South America.

Evidencia filogenética de una relación genética cercana entre la cepa peruana del virus de la laringotraqueítis infecciosa aviar VFAR-043 y dos cepas de campo con origen en los Estados Unidos. El virus de laringotraqueítis infecciosa aviar es el agente causal de una enfermedad aviar respiratoria aguda conocida como laringotraqueítis infecciosa que está asociada con pérdidas económicas en la industria avícola. La presencia del virus de la laringotraqueítis infecciosa ha sido ampliamente reportada en países de América del Sur; sin embargo, solamente una secuencia genómica completa (cepa VFAR-043) ha sido publicada recientemente y obtenida a partir de un brote en Perú. El objetivo de este estudio fue determinar la relación genética de la cepa peruana con otras cepas de diferentes regiones geográficas. El análisis filogenético reveló una cercana relación entre el virus VFAR-043 y dos cepas de los Estados Unidos (18746C5 y J2) usando el genoma completo y las regiones genómicas única larga (UL) y la región genómica única corta (UC). Posteriormente, estas tres secuencias genómicas fueron comparadas con la cepa de referencia del Departamento de Agricultura de los Estados Unidos (USDAref) para evaluar sus variaciones genéticas. Variaciones genéticas como polimorfismo de nucleótido único (con las siglas en inglés SNP) tanto de tipo sinónimo y no-sinónimo, inserciones, deleciones y variación de nucleótido en un codón fueron identificadas entre estas tres cepas (VFAR-043, 18746C5 y J2). Además, el análisis de los árboles filogenéticos usando secuencias genéticas de la región codificadora de US5 e ICP4 de aislamiento sudamericanos reveló que el virus VFAR-043 no mostró relación genética cercana con secuencias argentinas (US5) ni secuencias brasileras (ICP4) que están reportadas. No obstante, se observó una relación cercana entre el virus VFAR-043 y otro aislamiento peruano (USP-81) cuando se analizó la secuencia genética del gen ICP4. Todos estos resultados sugieren que los virus VFAR-043, 1874C5 y J2 están genéticamente relacionados. Estos hallazgos contribuyen al conocimiento de la epidemiologia del virus de la laringotraqueítis infecciosa aviar en América del Sur.