Campus-based #genomic #surveillance uncovers early emergence of a future dominant A(#H3N2) #influenza clade

Abstract

We conducted genomic surveillance of seasonal influenza during the 2022-2023 northern hemisphere flu season on a large university setting in Southwest Arizona USA to understand the diversity, evolution, and spread within a local environment and how it relates to national data. Through high-throughput sequencing and bioinformatics, we identified 100 positive samples (19%) from 516 clinical swabs collected at the student health clinic. We observed a dominance of subtype A(H3N2) which was consistent nationally for the 2022-2023 season. However, we found stark differences when examining subtype-specific H3 clades, which included an early dominance of clade 2a.3a.1 variants contrasting from country-level data in which 2b variants were most abundant. These variants might have contributed to the early seasonal peak on campus which lagged national trends by one month. We used phylodynamics to understand the timing, source, and impact of clade-specific introductions on campus and observed introductions of 2b variants from North America, Europe, and Asia in early 2022 which possibly contributed to its later-season dominance on campus towards the end of 2022. We also observed the impact of 2b variants in our Bayesian epidemiological model, as its its emergence and rapid rise coincided with the peak of infection on campus. We found several highly prevalent H3 mutations in known epitope sites that have been observed in multiple 3c.2a clades. In particular, we note the presence of N96S (N=57, 63%) which is a defining mutation of 2a.3 and 2a.3a.1 variants and has been shown to create a new potential N-glycosylation site in the globular head. We estimated vaccine effectiveness via an H3 epitope model with a range of 0.13-0.48 which overlaps with estimates for that year. Taken together, the abundance of antigenic drift mutations, in addition to our identification of numerous sequons found within HA1 (globular head) with high glycosylation potential likely contributed to moderate vaccine effectiveness on campus for that season. As 2a.3a.1 variants became nearly the exclusive H3 clade nationally in 2023-2024 as well as 2024-2025, our identification of their dominance on campus highlights the importance of monitoring local settings as potential early examples for national and influenza trajectories. By using high-throughput sequencing and multiple bioinformatics methods, we show the importance of genomic epidemiology in semi-closed, highly-dense university settings and its potential for early insight of seasonal influenza diversity at a national scale.

Source: MedRxIV, https://www.medrxiv.org/content/10.1101/2025.06.13.25329559v1

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#Neuroinvasive #Oropouche virus in a patient with #HIV from extra-Amazonian #Brazil

{Excerpt} A novel reassortant Oropouche virus (OROV) lineage (with medium [M], large [L], and small [S] RNA segments : M1L2S2) has driven Brazil's largest and most geographically widespread OROV epidemic , expanding beyond the endemic Amazon basin to establish local transmission across multiple Brazilian states and other previously unaffected Latin American countries . The rapid spread of this lineage underscores its evolutionary potential and reinforces its significance as a public health threat .1 Similar to chikungunya and Zika viruses, expanding arboviruses can exhibit unexpected clinical and epidemiological shifts , including vertical transmissions , neuroinvasive effects, and potentially fatal outcomes.2–4 Although OROV typically causes self-limited febrile illness, accumulating clinical and experimental evidence suggests neurotropic potential .5 This Correspondence describes the first confirmed case of neuroinvasive OROV infection caused by the emergent M1L2S2 lineage in ext...

Stability of #influenza viruses in the #milk of #cows and #sheep

Abstract In late 2023, H5N1 high pathogenicity avian influenza (HPAIV) started circulating in dairy cattle in the USA . High viral titres were detected in milk from infected cows , raising concerns about onwards human infections . Although pasteurisation was shown to effectively inactivate influenza viruses in milk, unpasteurised milk still poses a risk of infection, both from occupational exposure in dairies and from the consumption of raw milk. We therefore assessed how long influenza viruses could remain infectious for in milk without heat inactivation. We examined the stability of a panel of influenza viruses in milk , including a contemporary H5N1 HPAIV and a variety of other influenza A and D viruses. We incubated viruses in cows' milk under laboratory conditions : at room temperature to simulate exposure in dairies and at 4°C to simulate exposure to refrigerated raw milk. Following an isolated report of H5N1 viral RNA being detected in milk from a sheep in the UK , we also c...

#Evidence of #Viremia in Dairy #Cows Naturally Infected with #Influenza A {#H5N1} Virus, #California, #USA

Abstract We confirmed influenza A virus (IAV) by PCR in serum from 18 cows on 3 affected dairy farms in California, USA . Our findings indicate the presence of viremia and might help explain IAV transmission dynamics and shedding patterns in cows. An understanding of those dynamics could enable development of IAV mitigation strategies. Source: US Centers for Disease Control and Prevention, https://wwwnc.cdc.gov/eid/article/31/7/25-0134_article ____

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