A cross-sectional study of avian influenza A virus in Myanmar live bird markets: Detection of a newly introduced H9N2?

BACKGROUND: Zoonotic influenza surveillance in Myanmar is sparse, despite the risks of introduction of such viruses from neighboring countries that could impact the poultry industry and lead to spillover to humans. METHODS: In July and August 2019, our multi-institutional partnership conducted a One Health-oriented, cross-sectional surveillance (weekly for 3 weeks) for influenza A and influenza D viruses at the three largest live bird markets in Yangon, Myanmar. RESULTS: The 27 bioaerosols, 90 bird cage swabs, 90 bird oropharyngeals, and 90 human nasopharyngeal samples yielded molecular influenza A detections in 8 bioaerosols (30.0%), 16 bird cages (17.8%), 15 bird oropharyngeals (16.7%), and 1 human nasopharyngeal (1.1%) samples. No influenza D was detected. Seven of the influenza A virus detections were found to be subtype A/H9N2, and one human nasopharyngeal sample was found to be subtype A/H1pdm. Among all IAV-positive samples, three of the A/H9N2-positive samples yielded live viruses from egg culture and their whole genome sequences revealing they belonged to the G9/Y280 lineage of A/H9N2 viruses. Phylogenetic analyses showed that these A/H9N2 sequences clustered separately from A/H9N2 viruses that were previously detected in Myanmar, supporting the notion that A/H9N2 viruses similar to those seen in wider Southeast Asia may have been introduced to Myanmar on multiple occasions. CONCLUSIONS: These findings call for increased surveillance efforts in Myanmar to monitor for the introduction of novel influenza viruses in poultry, as well as possible reassortment and zoonotic virus transmission.

SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic.

COVID-19 was first diagnosed in Egypt on 14 February 2020. By the end of November 2021, over 333,840 cases and 18,832 deaths had been reported. As part of the national genomic surveillance, 1027 SARS-CoV-2 near whole-genomes were generated and published by the end of July 2021. Here we describe the genomic epidemiology of SARS-CoV-2 in Egypt over this period using a subset of 976 high-quality Egyptian genomes analyzed together with a representative set of global sequences within a phylogenetic framework. A single lineage, C.36, introduced early in the pandemic was responsible for most of the cases in Egypt. Furthermore, to remain dominant in the face of mounting immunity from previous infections and vaccinations, this lineage acquired several mutations known to confer an adaptive advantage. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and the need for enforcement of public health measures to prevent expansion of the existing lineages.

Continuing threat of influenza (H5N1) virus circulation in Egypt.

Reservoirs for the continuing influenza (H5N1) outbreaks in Egypt are ill-defined. Through active surveillance, we detected highly pathogenic influenza subtype H5 viruses in all poultry sectors; incidence was 5%. No other subtypes were found. Continued circulation of influenza (H5N1) viruses in various regions and poultry sectors perpetuates human exposure in Egypt.

The epidemiological and molecular aspects of influenza H5N1 viruses at the human-animal interface in Egypt.

With 119 confirmed cases between March 2006 and December 2010, Egypt ranks second among countries reporting human H5N1 influenza virus infections. In 2009-2010, Egypt reported 68 new human cases and became the new epicenter for H5N1 infections. We conducted an epidemiological and molecular analysis in order to better understand the situation in Egypt. The onset of new cases peaked annually during the winter and spring months, with majority of cases reported in the Nile Delta region. Most cases were less than 18 years old (62%) and females (60%). The overall case-fatality rate was 34% and significantly increased by age. There was a significant difference between the case-fatality rates among females and males. We observed a significant drop (p = 0.004) in case fatality rate in 2009 (10%) as compared to higher rates (36%-56%) in other years. Hospitalization within 2 or 3 days after onset of symptoms significantly decreased mortality. Molecular analysis showed that variations do occur among viruses isolated from birds as well as from humans in Egypt, and these mutations were especially noted in 2009 viruses. As the epidemiological profile of Egyptian cases differs from other countries, there is an urgent need to conduct prospective studies to enhance our understanding of incidence, prevalence, and determinants of virulence of human infections with avian H5N1 influenza viruses.