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Additional file 5: ML phylogenies of HMPV subgroup B1 sequences showing within country sequence diversity for Kenya, Gambia, Mali and South Africa sequences. Clustering patterns were determined by within-country sampling location (left panel) and or case/control status (right panel). For Gambia, only case/control clustering patterns were determined.

Additional file 7:ML phylogenies of RSV BA and GA2 sequences showing within country sequence diversity for Mali and South Africa sequences who’s within-country sampling information was available. Clustering patterns were determined by within-country sampling location (left panel) and or case/control status (right panel).

Additional file 4: ML phylogenies of HMPV and RSV G gene sequences collected from Kenya, Mali, Gambia, South Africa and Zambia. Sequences were subtyped based on clustering with with known subgroups or prototype sequences of HMPV and RSV retrieved from GenBank. Panel a: HMPV G gene sequences constructed using 231G gene sequences. Prototype sequences are coloured in red. The numbers next to branches indicate the bootstrap values. Subgroups were confirmed if sequences clustered with known subgroup-specific sequences within a major branch with > 70% bootstrap support. Panel b: RSV G ML phylogeny constructed using 627 unique gene sequences.

Parameter estimates, dN/dS ratios, positively selected sites and log likelihood scores for F and G gene nucleotide sequences for the HMPV subgroups identified between 2007 and 2016. (PDF 48 kb)

Phylogenetic analysis of Kilifi sequences and sequences retrieved from GenBank constructed using only full F gene sequences (1593â bp) to further asses the clustering of HMPV subgroups. A total 185 full F sequences were used. Sequences were subtyped using references sequences retrieved from GenBank. Reference sequences colored in red. The numbers next to branches indicate the bootstrap values, a branch with >â 70% bootstrap value was considered as a major branch. (PDF 44 kb)

Additional file 4: Table S1. Summaries of HMPV prevalence and incidence as reported in various publications.

Changes in G gene nucleotide sequences for sequences collected from Kilifi. Sequences were aligned by subgroup and by epidemic year for Clade A2b and A2c. Nucleotide differences were determined and indicated by vertical colored bars. Orange red represent Adenine (A), Crimson represent Thymine (T), Indigo represents Guanine (G) and slate blue represent Cytosine (C) nucleotide. (PDF 261 kb)

Additional file 1: Figure S1. The target positions in HMPV genomes for the set of 65 HMPV primers are presented. Green diamonds indicate forward primers, blue diamonds indicate reverse primers. Primers sites in representative A1, A2, B1 and B2 genomes are shown (HMPV A1: GenBank accession number AF371337, HMPV A2: FJ168779; HMPV B1: AY525843 and HMPV B2: FJ168778).

Additional file 1: Figure S1. The target positions in HMPV genomes for the set of 65 HMPV primers are presented. Green diamonds indicate forward primers, blue diamonds indicate reverse primers. Primers sites in representative A1, A2, B1 and B2 genomes are shown (HMPV A1: GenBank accession number AF371337, HMPV A2: FJ168779; HMPV B1: AY525843 and HMPV B2: FJ168778).

Newly designed F and G gene PCR and sequencing primers. (DOCX 15 kb)

Changes in G gene nucleotide sequences for sequences collected from Kilifi. Sequences were aligned by subgroup and by epidemic year for subgroups B1 and B2. Nucleotide differences were determined and indicated by vertical colored bars. Orange red represent Adenine (A), Crimson represent Thymine (T), Indigo represents Guanine (G) and slate blue represent Cytosine (C) nucleotide. (PDF 167 kb)

Additional file 4: Table S1. Summaries of HMPV prevalence and incidence as reported in various publications.

Phylogenetic analysis of Kilifi sequences and sequences retrieved from GenBank constructed using only full F gene sequences (1593â bp) to further asses the clustering of HMPV subgroups. A total 185 full F sequences were used. Sequences were subtyped using references sequences retrieved from GenBank. Reference sequences colored in red. The numbers next to branches indicate the bootstrap values, a branch with >â 70% bootstrap value was considered as a major branch. (PDF 44 kb)

Changes in G gene nucleotide sequences for sequences collected from Kilifi. Sequences were aligned by subgroup and by epidemic year for Clade A2b and A2c. Nucleotide differences were determined and indicated by vertical colored bars. Orange red represent Adenine (A), Crimson represent Thymine (T), Indigo represents Guanine (G) and slate blue represent Cytosine (C) nucleotide. (PDF 261 kb)

Additional file 2: HMPV G and RSV G genes PCR and sequencing primers used to generate the sequence data reported in this study.

Changes in G gene nucleotide sequences for sequences collected from Kilifi. Sequences were aligned by subgroup and by epidemic year for subgroups B1 and B2. Nucleotide differences were determined and indicated by vertical colored bars. Orange red represent Adenine (A), Crimson represent Thymine (T), Indigo represents Guanine (G) and slate blue represent Cytosine (C) nucleotide. (PDF 167 kb)

Newly designed F and G gene PCR and sequencing primers. (DOCX 15 kb)

Background: Globally, key subpopulations such as healthcare workers (HCWs) have a higher risk of contracting SARS-CoV-2. In Uganda, limited access to personal protective equipment amidst lack of clarity on the extent and pattern of the community disease burden may exacerbate this situation. We assessed SARS-CoV-2 antibody seroprevalence among high-risk sub-populations in South-central Uganda, including HCWs, persons within the general population previously reporting experiencing key COVID-19 like symptoms (fever, cough, loss of taste and smell) and archived plasma specimens collected between October 2019 â€" 18 th March 2020, prior to confirmation of COVID-19 in Uganda. Methods: From November 2020 - January 2021, we collected venous blood from HCWs at selected health facilities in South-Central Uganda and from population-cohort participants who reported specific COVID-19 like symptoms in a prior phone-based survey conducted (between May to August 2020) during the first national lockdown. Pre-lockdown plasma collected (between October 2019 and March 18 th , 2020) from individuals considered high risk for SARS-CoV-2 infection was retrieved. Specimens were tested for antibodies to SARS-CoV-2 using the CoronaChek TM rapid COVID-19 IgM/IgG lateral flow test assay. IgM only positive samples were confirmed using a chemiluminescent microparticle immunoassay (CMIA) (Architect AdviseDx SARS-CoV-2 IgM) which targets the spike protein. SARS-CoV-2 exposure was defined as either confirmed IgM, both IgM and IgG or sole IgG positivity. Results: The seroprevalence of antibodies to SARS-CoV-2 in HCWs was 21.1% [95%CI: 18.2-24.2]. Of the phone-based survey participants, 11.9% [95%CI: 8.0-16.8] had antibodies to SARS-CoV-2. Among 636 pre-lockdown plasma specimens, 1.7% [95%CI: 0.9-3.1] were reactive. Conclusions: Findings suggest a high seroprevalence of antibodies to SARS-CoV-2 among HCWs and substantial exposure in persons presenting with specific COVID-19 like symptoms in the general population of South-central Uganda. Based on current limitations in serological test confirmation, it remains unclear whether pre-lockdown seropositivity implies prior SARS-CoV-2 exposure in Uganda.