Genomic epidemiology and evolution of rhinovirus in western Washington State, 2021-22 (preprint)

Background: Human rhinoviruses (RV) primarily cause the common cold, but infection outcomes vary from subclinical to severe cases, including asthma exacerbations and fatal pneumonia in immunocompromised individuals. To date, therapeutic strategies have been hindered by the high diversity of serotypes. Global surveillance efforts have traditionally focused on sequencing VP1 or VP2/VP4 genetic regions, leaving gaps in understanding RV true genomic diversity. Methods: We sequenced 1,003 RV genomes from nasal swabs of symptomatic and asymptomatic individuals to explore viral evolution during two epidemiologically distinct periods in Washington State: when the COVID 19 pandemic affected the circulation of other seasonal respiratory viruses except for RV (from February to July 2021), and when the seasonal viruses reemerged with the severe RSV and influenza outbreak (November and December 2022). We constructed maximum likelihood and BEAST phylodynamic trees to characterize intra-genotype evolution. Results: We detected 100 of 168 known genotypes, identified two new genotypes (A111 and C59), and observed inter-genotypic recombination and genotype cluster swapping from 2021 to 2022. We found a significant association between the presence of symptoms and viral load, but not with RV species or genotype. Phylodynamic trees, polyprotein selection pressure, and Shannon diversity revealed co-circulation of divergent clades within genotypes with high amino acid constraints throughout polyprotein. Discussion: Our study underscores the dynamic nature of RV genomic epidemiology within a localized geographic region, as more than 20% of existing genotypes within each RV species co-circulated each month. Our findings also emphasize the importance of investigating correlations between rhinovirus genotypes and serotypes to understand long-term immunity and cross-protection.

The unified proposal for classification of human respiratory syncytial virus below the subgroup level (preprint)

A globally implemented unified classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. Here, we formulate the global consensus of HRSV classification based on the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to NCBI and GISAID up to March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B, providing guidelines for prospective lineages definition. Our classification demonstrated robustness in its applicability to both complete and partial genomes. In addition, it allowed the observation of notable lineage replacements and the identification of lineages exclusively detected since the COVID-19 pandemic. We envision that this unified HRSV classification proposal will strengthen and facilitate HRSV molecular epidemiology on a global scale.

Genomic characterization of respiratory syncytial virus 2022-2023 outbreak in Washington State, USA (preprint)

Mitigation measures against the COVID-19 pandemic affected the RSV seasonality and led to an unexpectedly high number of RSV cases in Washington State since October 2022. Here we describe the RSV genomic characteristics and evolutionary relationship of 2022 outbreak compared to the previous RSV outbreaks in the region and globally.

RSV reemergence in Argentina since the SARS-CoV-2 pandemic.

INTRODUCTION: The community mitigation measures taken because of the COVID-19 pandemic had side effects on the circulation of the most frequent respiratory viruses during 2020. In the case of respiratory syncytial virus (RSV), an important paediatric pathogen, a decrease in the number of cases and delayed outbreaks was previously described. AIM AND METHODS: The genetic characteristics of the RSV circulating strains in paediatric patients in Buenos Aires, Argentina before and during the COVID-19 pandemic were studied. RSV (+) samples taken from hospitalised patients with respiratory tract infections (2018- 2021) were analysed through G gene sequencing and evolutionary analyses. RESULTS: No RSV hospitalised paediatric patients were registered in Buenos Aires during 2020; however, RSV reemerged in 2021 with a lower number of cases and a delayed outbreak, peaking in July-August. A total of 147 G gene sequences were analysed. RSV-B (N = 85) predominated during 2018 and 2021 whereas in 2019 RSV-A were more prevalent (N = 62). All RSV-A sequences were ON1-like strains, and all RSV-B were BA-like. Phylogenetic analyses showed that the same genetic lineages circulated before and after 2020, but RSVs from 2021 corresponded to new viral introductions rather than cryptic circulation of the previous genetic clusters in Buenos Aires during 2020. CONCLUSIONS: Following the reopening of borders, the reemergence of RSV in Argentina brought new viral introductions from other countries. Therefore, it is important to continue a deep global molecular surveillance to characterise RSV strains in post-pandemic circulation with an impact in future vaccine implementation.

SARS-CoV-2 genomic surveillance enables the identification of Delta/Omicron co-infections in Argentina. (preprint)

Molecular surveillance of SARS-CoV-2 is crucial to early detect new variants and lineages. In addition, detection of coinfections with more than one SARS-CoV-2 lineage have been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2067 RNA samples (Ct>30) obtained during December 2021 and January 2022 from Cordoba province, Argentina, by real time RT-PCR specific for VOC/VOI relevant mutations (TaqMan SARS-CoV-2 Mutation Panel, Applied Biosystems). The following distribution of variants was obtained: Omicron (54.9%), Delta (44.2%) and Lambda (0.8%). Three samples (0.1%), obtained the last week of December, presented a profile compatible with a Delta/Omicron co-infection. One of them was sequenced by NGS-Illumina, obtaining reads for both VOCs. One of the studied patients presented severe symptoms, although he was not vaccinated and presented risk factors (older than 60 years, arterial hypertension). We describe for the first time in Argentina, the identification of cases of co-infection with two SARS-CoV-2 lineages, VOCs Delta and Omicron, during the third COVID-19 wave in the country (a high viral circulation period), when Delta and Omicron co-circulated. Our findings highlight the importance of continuing with molecular surveillance and co-detection studies of VOC/VOIs, in order to elucidate possible recombination events and the emergence of new variants.

Surveillance of SARS-CoV-2 variants in Argentina: detection of Alpha, Gamma, Lambda, Epsilon and Zeta in locally transmitted and imported cases (preprint)

Molecular surveillance of SARS-CoV-2 variants was performed on a total of 2,406 samples from the capital city and nine provinces of Argentina, during 30 epidemiological weeks (EW) that covered the end of the first wave and the beginning of the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 20/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the simultaneous identification of signature mutations associated with worldwide circulating variants. In addition, whole SARS-CoV-2 genome sequences were obtained from 456 samples. The main variants found were Gamma, Lambda and Alpha, and to a lesser extent, Zeta and Epsilon. Whereas Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires (MABA), although showing a heterogeneous distribution along this region. This cost-effective surveillance protocol allowed for a rapid response in a limited access to resources scenario, added information on the expansion of the Lambda variant in South America and contributed to the implementation of public health measures to control the disease spread in Argentina.