Since 2004, the U.S. Centers for Disease Control and Prevention (CDC) Influenza Division (ID) has supported seven countries in the Eastern Mediterranean region and the World Health Organization Regional Office for the Eastern Mediterranean to establish and strengthen influenza surveillance. There has been substantial growth in influenza surveillance capacities in the region over two decades that demonstrates commitment by national governments to strengthen national programs and contribute to global influenza surveillance. CDC ID remains committed to continuing support to the region and supporting partners to translate surveillance data into policies and programs effectively.

In 2019, the Louisiana Department of Health reported an early influenza B/Victoria (B/VIC) virus outbreak. As it was an atypically large outbreak, we deployed to Louisiana to investigate it using genomics and a triplex real-time RT-PCR assay to detect three antigenically distinct B/VIC lineage variant viruses. The investigation indicated that B/VIC V1A.3 subclade, containing a three amino acid deletion in the hemagglutinin and known to be antigenically distinct to the B/Colorado/06/2017 vaccine virus, was the most prevalent circulating virus within the specimens tested. This work underscores the value of portable diagnostics and sequencing platforms for rapid, onsite pathogen characterization.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) enters the host cell by binding to angiotensin-converting enzyme 2 (ACE2). While evolutionarily conserved, ACE2 glycoproteins differ across various species and differential interactions with Spike (S) glycoproteins of SARS-CoV-2 viruses impact species specificity. Reverse zoonoses led to SARS-CoV-2 outbreaks on multiple American mink ( Mustela vison) farms during the pandemic and gave rise to mink-associated S substitutions known for transmissibility between mink and zoonotic transmission to humans. In this study, we used bio-layer interferometry (BLI) to discern the differences in binding affinity between multiple human and mink-derived S glycoproteins of SARS-CoV-2 and their respective ACE2 glycoproteins. Further, we conducted a structural analysis of a mink variant S glycoprotein and American mink ACE2 (mvACE2) using cryo-electron microscopy (cryo-EM), revealing four distinct conformations. We discovered a novel intermediary conformation where the mvACE2 glycoprotein is bound to the receptor-binding domain (RBD) of the S glycoprotein in a “down” position, approximately 34° lower than previously reported “up” RBD. Finally, we compared residue interactions in the S-ACE2 complex interface of S glycoprotein conformations with varying RBD orientations. These findings provide valuable insights into the molecular mechanisms of SARS-CoV-2 entry.

Global influenza virus circulation declined and has been below traditional seasonal levels during the COVID-19 pandemic.1-3 We reviewed WHO influenza surveillance outputs from May 1-December 31, 2020 (epidemiologic weeks 18-53) from tropical Asian countries. For each country we report influenza surveillance specimens tested, and the percentage positive for influenza, by type and subtype. We compared current data to historical data from 2015-2019 in order to place the current season in historical context. Twelve included countries tested 17,407 surveillance specimens, with 592 (3.4%) testing positive for influenza viruses. From April 27-July 26, 2020 (epidemiologic weeks 18-30), specimens tested decreased from an average of 14,102 per year in 2015-2019 to 3,969 (71.9% decrease) and influenza positivity from 22% to <1%. During weeks 31-53, specimens tested decreased from an average of 24,782 per year in 2015-2019 to 13,438 (45.8% decrease) and influenza positivity from 18% to 4%. In six countries that maintained testing of surveillance specimens for >90% of weeks, influenza circulation was unseasonably low, or absent, during weeks 18-30, 2020. However, during weeks 31-53, the percentage of surveillance specimens testing positive for influenza approached or reached positivity rates of 2015-2019 in Bangladesh and Cambodia; and increased but remained lower than historical positivity in Lao PDR and Viet Nam. The data presented here are a reminder that the low levels of influenza circulation in the northern hemisphere in summer 2020 may not necessarily persist into the upcoming influenza season, and influenza surveillance and prevention strategies should continue as planned and not be delayed.