Svetlana Colac, Valeria Ceban, Livia Țapu, Veronica Burlac, Nicolae Jelamschi, Olga Burduniuc
The study provides a descriptive genomic characterization of a laboratory-selected subset and illustrates a workflow linking molecular testing to sequencing. The findings should not be interpreted as estimates of national clade prevalence, geographical distribution, or A(H1N1)pdm09/SARS-CoV-2 co-infection frequency.
BACKGROUND: Genomic sequencing can complement routine influenza surveillance by enabling clade-level characterization of selected specimens and the genomic characterization of mixed viral specimens. This descriptive laboratory-based study characterized influenza A-positive respiratory specimens collected through routine surveillance in the Republic of Moldova and selected for sequencing.
METHODS: Between October 2025 and February 2026, 1,081 respiratory specimens were screened by multiplex real-time reverse transcription polymerase chain reaction for influenza A, influenza B, and SARS-CoV-2. Of 291 influenza A-positive specimens, 174 had cycle-threshold values ≤27, and 38 were selected for hybrid-capture sequencing based on repeat cycle-threshold values and technical suitability. Consensus sequences were analyzed with Nextclade, and the SARS-CoV-2 component of one mixed specimen was additionally assessed using Pangolin.
RESULTS: All 38 selected specimens yielded analyzable influenza A hemagglutinin sequences, with hemagglutinin-segment coverage ranging from 87.6% to 100%. The dataset comprised 32 A(H3N2) specimens, five A(H1N1)pdm09 specimens, and one mixed A(H1N1)pdm09/SARS-CoV-2 specimen. All A(H3N2) hemagglutinin sequences were assigned to clade K, subclade 2a.3a.1. The six A(H1N1)pdm09 hemagglutinin components were assigned to clade D.3.1 (n = 2) or D.3.1.1 (n = 4). The SARS-CoV-2 consensus was assigned to Nextclade clade 25I; poor overall sequence quality limited confidence in fine-scale lineage assignment and precluded robust interpretation of private mutations.
CONCLUSION: The study provides a descriptive genomic characterization of a laboratory-selected subset and illustrates a workflow linking molecular testing to sequencing. The findings should not be interpreted as estimates of national clade prevalence, geographical distribution, or A(H1N1)pdm09/SARS-CoV-2 co-infection frequency.