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Highly pathogenic avian influenza viruses (HPAIVs) are a permanent threat to public health due to their potential zoonotic transmission. Among HPAIVs, Influenza A H5 viruses have caused outbreaks in poultry and wild birds worldwide,1 and virus clade 2.3.4.4b outbreaks have been reported in Europe, Asia, Africa and North America since 2020, accounting for an unprecedented number of bird deaths.2 The mutation ability to infect new species, including humans, makes HPAIVs of high concern.3–5 Since 2020, six human cases of clade 2.3.4.4b viruses have been reported to WHO from China, Spain, UK, USA and Vietnam.6 During late 2022, H5N1 outbreaks were declared in South America and clade 2.3.4.4b was identified for the first time in the region.6,7 On 9 January 2023, the WHO was notified of a human infection by an avian Influenza A(H5) virus in Ecuador (https://www.who.int/emergencies/disease-outbreak-news/item/2023-DON434). The patient was a 9-year-old girl without co-morbidities from Bolivar Province, who was admitted to a hospital due to severe flu symptoms in 30 December 2022. She was transferred to the ICU of a paediatric hospital on 3 January 2023 due to complications with septic shock and pneumonia. She received complex support antiviral treatment, including oseltamivir, managing to improve her critical condition; She continued in interdisciplinary management with favorable progress and was finally discharged from the hospital. Nasopharyngeal and bronchoalveolar samples were collected on 5 and 7 January 2023 and were sent to the laboratory in the Ecuadorian National Institute of Public Health in Ecuador for RT-qPCR testing with the CDC Influenza Virus Real-Time RT-PCR Panel and Influenza A/H5 (Asian Lineage) Subtyping Panel. Both samples resulted positive for FluA (Ct of 33.2 and 34.6) and H5 (Ct of 34.2 and 36.1). Samples were sent to the Regional Reference Lab (Center for Diseases Control and Prevention of the USA) that confirmed our results. According to the epidemiological investigation, the girl was in contact with backyard poultry that died without apparent cause. Moreover, several incidents of dead backyard poultry have been reported in Bolivar Province, and these were close to the origin of H5N1 clade2.3.4.4b outbreak in Ecuador. No family members tested positive for H5 flu. This is the first reported case of human infection by avian Influenza A(H5) virus in Latin America and is the first human case reported worldwide in 2023.6 To study the origin of this H5N1 outbreak, an alignment of 32 sequences in total of the hemagglutinin (HA) gene (Figure 1) was created with all isolated sequences from Ecuador by blast them to closed related sequences from GenBank-NCBI by using software Geneious Prime® v. 2023.0.1 by implementing the package MAFFT alignment method. The Hasegawa-Kishino-Yano substitution model was determined as the best fitter model for the alignment with the software jModelTest 2.1.10. Phylogenetic reconstruction was performed with the Markov Chain Monte Carlo (MCMC) Bayesian approach implemented in BEAST version 2.7.1 through a non-parametric Bayesian Skyline (Piecewise-constant) coalescent model with a Strict molecular clock method. MCMC was developed with 20 million generations for the alignment, which were subsampled every 1000 generations by applying a Random as the starting tree. Moreover, a Marginal likelihood estimation (MLE) using path sampling/stepping-stone sampling, which performs an additional analysis after the standard MCMC chain has finished, was implemented. Log files were inspected and were monitored through the with Tracer version 1.7.1 to evaluate the ESS support values for all the parameters, which super-passed the minimum requirements. The MCMC/MLE analysis output was summarized using TreeAnnotator software included in the Beast package. The maximum Clade Credibility tree was produced after discarding 10% of burn-in. The final tree was visualized through FigTree version 1.4.4 (Figure 1). Phylogenetic analysis based on the sequences for hemagglutinin (HA) gene. The H5N1 strain circulating in Ecuador belongs to the clade 2.3.4.4b responsible for the current avian flu outbreaks in Europe and the Americas in 2020-2023. The diagram shows the wide range of cross-species transmission of the clade 2.3.4.4b, including in various occasions human and other mammal species hosts (the sequences for the suggested origin “outgroup” from Ghana and England in 2021 are included in the analysis; the dotted line shows the human case from Ecuador assuming the same viral strain detected in poultry). The H5N1 variant identified in Peru, Venezuela, Chile, Mexico and Ecuador belongs to the same clade 2.3.4.4b that was also isolated from infected humans in UK, Spain and USA in 2021–22. The same variant was also isolated across several wild bird species and also from a dolphin in USA, red foxes and skunks in Canada and minks from a farm in Spain, implying a transmission across multiple host species, including mammals, from the initial outbreak in Europe to America (Figure 1). Despite several sequencing attempts, no viral sequences from the H5 human case in Ecuador were recovered, due to the time period between symptoms onset and sample collection. Moreover, the surveillance among people exposed to poultry is limited to symptomatic individuals in Ecuador, and genome sequencing is still expensive in the context of low and middle income countries, so only seven poultry and wild birds samples have been processed in the Ecuadorian National Institute of Public Health in Ecuador for genome sequencing. This case shows the need to rise concern among South American health authorities to support HPAIVs genomic surveillance, as an early identification of circulating strains would assist the WHO programme for HPAIVs candidate vaccine viruses. For instance, the virus circulating in South America is grouped in the same clade with the new 2.3.4.4b candidate vaccine virus (Figure 1). Despite the high number of poultry outbreaks declared worldwide since 2020, only seven cases of human infection with clade 2.3.4.4b virus have been reported. Nevertheless, three of these cases had a severe or fatal outcome.6 Although, there is limited evidence of mutations associated with co-speciation in mammals and no sustained human-to-human transmission has been documented, the reported mink to mink transmission of the H5N1 clade 2.3.4.4b5 warns about the danger associated with the current viral strain circulating in South America. We call for action about the importance of a worldwide HPAIVs genomic surveillance from a One Health perspective, including poultry, wild birds and mammals, beside humans. In a scenario of weak surveillance programmes and low sanitation as is usual in low and middle income countries, a high risk of uncontrolled zoonotic exposure to HPAIVs may lead to the emergence of a new variant transmitted from human to human, representing a pandemic threat. All the authors contributed to the conceptualization, experimental procedures and data collection and approved the final version of the manuscript. A.A.-N. and A.B. performed the phylogenetic analysis and contributed to the writing of the final version of the manuscript. M.A.G.-B. wrote the first draft and final version of the manuscript. No specific funding was allocated for this study. We thank ‘Agrocalidad’ and ‘Ministerio de Salud Pública de Ecuador’ for their efforts to improve a multidisciplinary avian flu surveillance programme and also the medical team from Hospital Baca Ortiz for its successful patient management. We thank PAHO for providing reagents for avian flu diagnosis to ‘Laboratorio Nacional de Referencia para Influenza y Otros Virus Respiratorios’ from ‘Instituto Nacional de Salud Pública e Investigación’‘Leopoldo Izquieta Pérez’. None declared.
Bruno et al. (Tue,) studied this question.