1. Introduction
Human enteroviral infections are contracted predominantly via the faecal-oral route and exhibit a broad spectrum of disease ranging from asymptomatic or self-limiting illness through to high clinical consequence and associated mortality [
1,
2]. The causative Enteroviruses (EV) can be subcategorised into four species, EV-A to EV-D comprising over 100 types and are more prevalent within younger age groups, with severe outcomes including acute flaccid myelitis, endocarditis, and meningitis [
3,
4]. Less severe and more frequent enteroviral disease manifestations include hand, foot and mouth disease (HFMD), presenting classically with short-lived combinations of low-grade fever, malaise, a maculopapular rash or blisters on the hands, soles and buttocks and ulcerative lesions of the throat, mouth and tongue [
5].
EV-A types are the leading cause of HFMD, principally EV-A71 and several members of the genetically diverse Coxsackievirus (CV) grouping CVA6, CVA10 and CVA16 [
6]. Since 2008, CVA6 has been increasingly diagnosed in HFMD outbreaks across the world [
7,
8,
9,
10,
11]. These recent epidemics have featured an atypical HFMD presentation of a more disseminated rash or principally herpangina [
12,
13,
14,
15] and can include a significant number of affected adults [
16,
17]. Onychomadesis - the separation of the nail from its matrix due to cessation in growth - can also be observed in atypical HFMD [
18,
19], occurring circa 8 weeks post infection in the majority of cases [
20]. In rarer instances, CVA6 infection can lead to more severe complications like aseptic meningitis, encephalitis, acute flaccid myelitis and sometimes fatality [
17,
21,
22,
23]. Even though the majority of CVA6 infections occur without sequalae, higher mortality rates are often observed amongst the immunosuppressed due to the development of neurological complications [
24]. The high prevalence of CVA6 infection combined with the potential for severity has prompted interest in the development of a vaccine [
25].
HFMD is routinely diagnosed by clinical presentation, however, the causative virus can be confirmed via molecular methods involving the amplification and detection of the viral genome. Specific molecular assays targeting the 5’ UTR have previously been successful at identifying the presence of enteroviruses [
26], however due to genetic drift occurring mainly within the capsid coding region and recombination [
27,
28], sequencing the VP1 gene is used predominantly to determine EV types [
29,
30]. CVA6 detection can be accomplished via analysis of skin and nasopharyngeal swabs, stool samples and / or fluid extracted from cutaneous lesions and vesicles. The European Union and the USA currently have no mandatory legislations with regards to notifying incidences of HFMD, causing difficulties in surveillance and identifying transmission trends of this enterovirus [
31,
32]. In contrast HFMD is a notifiable disease in China, allowing national surveillance and enterovirus prevalence to be identified [
33].
CVA6 has a single stranded positive sense RNA genome comprised of approximately 7400 bases and can be distinguished into four genotypes A-D, further subcategorised into sub-genotypes including B1, B2, C1, C2 and D1-3 [
34]. Sub-genotype D3 has recently been evidenced as the most prevalent sub-genotype [
35,
36,
37], however the non-pharmaceutical interventions of the SARS-CoV-2 pandemic may have inadvertently affected circulation of enteroviruses including CVA6 [
38]. We thus aimed to investigate the genetic and clinical epidemiology of CVA6 diagnosed in our regional UK hospital in epidemic seasons before and after the emergence of SARS-CoV-2.
2. Materials and Methods
The study was conducted in two periods: initially between 1st September to 17th December 2018 when a significant Enterovirus D68 epidemic was experienced and previously reported [
39]. A second period followed between 11th May 2021 and 26th April 2023, when our diagnostic laboratory re-commenced enteroviral testing post-pandemic and sought to evaluate routine enteroviral typing. Whilst the precise start and end of the SARS-CoV-2 pandemic are open to debate, to simplify the narrative in this study, all 2021-2023 samples are referred to as ‘post-pandemic’.
Samples were screened for enteroviral infection using both commercial and in-house assays as described previously [
30,
39]. Briefly, samples were determined EV-positive by the commercial clinical assay (AusDiagnostics, Australia) as part of the routine care diagnostic pathway. Where available, surplus nucleic acid was re-screened using in house assays targeting partial VP1 and 5’ NCR genomic regions and candidate positives were confirmed by Sanger sequencing [
29,
30]. Some patients had more than one sample taken and were thus sequenced more than once also. Additionally, a minority of diagnostic samples were submitted for typing at the National Reference Laboratory, either confirming CVA6 infection or independently identifying further CVA6 in 4 cases without residual material available.
Confirmed CVA6 positive samples were then further amplified with two novel PCR assays targeting overlapping genomic regions covering the entire VP1 gene, based on all CVA6 lineage exemplars as presented by Bian et al 2015 [
40] using MEGA7 [
41] and Primer3 (
https://primer3.ut.ee/). This pilot amplification returned inconsistent results, with approximately 50% amplification success (data not shown), but Sanger sequencing and phylogenetic analysis of successfully amplified samples indicated all were of the globally most common lineage D3 [
37]. Therefore, the primers were modified and / or redesigned to specifically target CVA6 lineage D3 based on lineage D3 reference sequences and a single contig generated from a study sample in the preliminary VP1 amplification.
Final primer pairs employed to amplify and sequence full length VP1 were set A: CVA6D3_VP1Af AGACTGGAGGGGTATACGACT (positions 2258 – 2278 on CVA6 Kyoto5 D3 strain, GenBank accession number AB779618.1) and CVA6D3_VP1Ar GGTATGATTTYCTGCTATCCGG (2935 – 2914) generating a product size 678bp; and set B: CVA6D3_VP1Bf GCGCTTTGAYGCCGAGTT (2814 – 2831) and CVA6D3_VP1Br TCTCGTGAGCTACTTTCCCA (3473 – 3454) generating a product size of 660bp. Both products were amplified in 20µl reactions with HotStarTaq (QIAGEN) as per manufacturer’s recommendations, 1-2 µl hexamer-primed cDNA template and 200 µM forward and reverse primers, thermocycled as follows: 95
oC for 15 min then 55 cycles of 95
oC for 20 s, 55
oC 20s and 72
oC for 60s. PCR products of the expected size when visualised by gel electrophoresis were sequenced with primers CVA6D3_VP1Ar and CVA6D3_VP1Bf as appropriate. Sequences were basecalled using FinchTV and identity was preliminarily assessed using NCBI Standard Nucleotide BLAST (BLASTn) and the Genome Detective online Enterovirus Genotyping Tool (Version 2.9) [
42].
Sequences were compared to a global reference dataset generated by retrieving all available full length VP1 lineage D sequences CVA6 (n = 4358) from GenBank in December 2023, as well as a smaller cohort to identify lineage [
35]. These were aligned with the study sequences using Geneious software, and a phylogenetic tree was assembled in IQ tree 2 [
43] using the SYM+I+R6 model and 1000 SH-aLRT bootstraps, then annotated using FigTree (
http://tree.bio.ed.ac.uk/software/figtree/). Complete CVA6 sequences from this study are deposited on GenBank under accession numbers MZ576353 - MZ576381 and ABXXXXXX – ABXXXXXX.
Available clinical data was audited under local study number 23-005C, as approved by the Nottingham University Hospitals NHS Trust. As part of the anonymisation process of clinical data export, ages were only recorded in discrete months or years. Without formal prospective categorisation, rash type reporting was highly varied from multiple clinical sources and degrees of experience, including: Vesicular (n = 30), eczema coxsackium (n = 18), HFMD (n = 8), crusted lesions (n = 2) impetigo (n = 2), as well as macular, maculopapular, nappy rash, papular, combinations of the aforementioned or type not stated (n = 16). Therefore, this data category was reduced to the binary presence or absence of a rash for statistical investigation, and accordingly no distinction could be made between classical and atypical HFMD.
Swabs taken from any external anatomy were designated as skin swabs and those involving any sampling of the throat e.g. nose and throat as oral swabs. Any non-skin or oral cavity specimen, including whole blood, faeces, nasopharyngeal aspirates (all n = 2) and ocular swabs, bronchoalveolar lavage and sputum (all n = 1) were grouped together as ‘other’ for analyses.
Statistical analyses were performed on the available clinical data segregated by the time of sample acquisition. Samples from 2018 were compared against those sampled in 2021-2023. Contingency analyses of categorical data were performed by χ2 test, as implemented in GraphPad Prism 10.3.1.
4. Discussion
Our study covered the two sampling periods, both before and after the emergence of SARS-CoV-2 where we undertook universal in-house enteroviral typing, rather than selective referral to a reference laboratory service [
30,
39]. Whilst a key objective in the pre-pandemic era was to assess the impact of EV-D68 in a hospital setting [
39,
49], it became apparent that CVA6 was the second-most prevalent enterovirus detected and thus demanded further investigation. This finding was re-enforced when we undertook a post-pandemic pilot project to determine the genotype of all diagnosed infections. High prevalence of CVA6 amongst clinically diagnosed enteroviral infections was in agreement with other universal screening studies, most significantly and relevantly in the recent and largest study of enteroviral infections in Europe to date [
4] but also in the US [
50] and worldwide in general [
40].
The seasonality of enterovirus infections can sometimes be oversimplified as a broadly summer infection [
51], which may be true for some types but not others [
4]. However, here we demonstrate that, in agreement with others, CVA6 undoubtedly peaks in the Autumn in the UK [
52]. A subtle shift in transmission peak was observed in 2021, potentially due to the unprecedented non-pharmaceutical intervention measures introduced to limit SARS-CoV-2 transmission in the UK and elsewhere globally [
44]. Diminished pandemic transmission of other enteroviruses has also been recorded [
49] with an accompanying uncertainty about infection rates and severity as interventional measures were lifted with a generally older susceptible population [
53].
Age at CVA6 diagnosis broadly followed trends reported elsewhere, with a large UK-based cohort also finding most (52%) to be 1–5 years of age and a further quarter (23%) to be between 4 and 12 months old [
52], as well as a similar demographic more broadly in Europe [
4]. Interestingly our hypothesized but not statistically significant study trend of children acquiring CVA6 slightly later in life in the immediately post-pandemic era was in contradiction to a similar study in the Netherlands [
38].
By comparison, 2021 Respiratory Syncytial Virus infections were recorded earlier than expected and also with increased severity [
54,
55]. Perturbance of typical viral transmission patterns has been assessed most intensively with Influenza epidemiology [
56] and observed most significantly with the lack of detection of Influenza B Yamagata lineage since March 2020 [
57]. Although influenza epidemics were observed to be of lower intensity and shorter in a study of nine Asian countries in 2021 [
58], our data indicated a similar size CVA6 infection burden in 2021 compared to 2018. The greater proportion of males presenting at circa 60% in each group appears to be a general feature of HFMD as this was in close agreement with a predominantly EV-A71- and CVA16-causal HFMD cohort in China [
59].
Whilst our limited CVA6 cohort split across three epidemic seasons with non-uniformly recorded clinical details was unable to fully probe disease manifestations, particularly in terms of rash appearance, others have done so comprehensively in contemporary European pre-pandemic cohorts, finding an approximately 3 to 1 caseload of atypical rather than typical HFMD presentation [
37]. Instead we focused on more universal parameters of infection and their variability pre- and post-pandemic, finding an elevated respiratory tract involvement in 2018, supported by findings in linked parameters with more respiratory tract sampling and lesser rash observation and HFMD primary diagnosis in this year. The pre-pandemic sample profile allies more closely with results from the broad European cohort of Bubba and colleagues, with CVA6 detected by skin swab in approximately half of all cases and secondarily in the respiratory tract in approximately a quarter [
4]. Others have found CVA6 to be the most commonly detected enterovirus of the respiratory tract [
60]. In another extensive, but more closely matched study set exclusively in the UK from 2006 to 2017 (>1000 CVA6 cases), the sample set comprised 73.5% skin (and vesicle) swabs and just 13.2% respiratory specimens, similar to our more disparate post-pandemic sampling [
52].
The limited sampling from non-skin/oral sites and associated non-respiratory/HFMD principal diagnosis seen in our results, was reflected elsewhere [
4,
52], although the circa one-third febrile cases recorded in both pre- and post-pandemic groups was approximately three-fold greater than the European average [
4]. However, neurological manifestations such as the febrile convulsions we saw in the smaller 2018 group have been significant proportions of other CVA6 cohorts [
60]. The severe neurological complication Acute Flaccid Paralysis (AFP) was also seen in CVA6 cases in China earlier in the mid-2000s [
35], although our sole case was co-infected with EV-D68, which may have been the principal causative agent [
39,
61]. EV-D68 and CVA6 co-infection has also been observed previously presenting classical symptomology of both enteroviruses [
62]. Given that these viruses were the most prevalent in our recent surveillance pre- and post-pandemic here and elsewhere [
39], occasional co-infections should accordingly be expected, as should co-infection by intra-typic strains of CVA6 that must have facilitated the extensive genomic recombination characterised in whole genome sequencing studies [
27,
28,
37].
We confirmed the recent dominance of CVA6 genotype D3 in the UK as reported both elsewhere in continental Europe [
13,
37] and China [
35], although our exclusively VP1 sequencing approach lacked the ability to further characterise the aforementioned genomic recombinants hypothesised to enhance its post-millennium emergence and pathogenicity [
27,
37,
63]. However, whole genome sequencing only further exacerbates the apparent complexity of strains beyond the genotype D3 designation that was apparent in our phylogenetic analyses. Whilst we observed less intermingling between study and non-study sequences post-pandemic, this is likely to be at least in part an artefactual result of limited available reference material to date as many viral sequencing laboratories have diverted time and resources to prioritise SARS-CoV-2 studies.
In the better-sampled pre-pandemic era, considerable sub-genotype diversity and by implication labyrinthine transmission chains were indicated. Closely sampled CVA6 genomes from our regional UK centre were more closely related to those in other countries or even continents than each other in many instances, as was also the case in our related EV-D68 study [
39]. The intercontinental viral transmission illustrated by groups such as ours during the emergence of SARS-CoV-2 [
64], was again demonstrated with the likely import of an East Asian CVA6 sub-lineage alongside an East-Asian EV-D68 sub-lineage [
39], most surprisingly in the same co-infected returning traveller. Where pre-pandemic study sequences were most closely related, or even identical in the VP1 region covered, clinical auditing indicated no obvious clues to epidemiological linkage, further emphasising hidden subclinical transmission events and the unsampled burden of infection. A study sampled in the preceding years of 2016-17 in Australia also showed a similarly mixed epidemiological picture of genetically isolated viruses, alongside clusters suggestive of endemic transmission chains across seasons [
48].
Others have attempted to compare enteroviral genetic diversity pre- and post-pandemic, finding a reduction in genetic variability may have occurred with the lockdown measures introduced, although not notably in CVA6 [
38]. Whilst suitably cautious, waiting for additional evidence from further complementary studies such as presented here, they equally note that genetic change arising from transmission bottlenecks may indeed become clinically relevant in the future.
In conclusion, the global epidemiology of viral infections is experiencing an unprecedented era, following a phase of restrictive measures and their subsequent relaxation, leaving an atypical global immune landscape within which to renew transmission [
65]. Our study indicates this phenomenon has indeed perturbed CVA6 in the UK, with evidence of an effect on circulating lineages, their peak epidemic season and their associated clinical manifestation. The global capability in virological surveillance demonstrated during the SARS-CoV-2 pandemic could be increasingly applied to monitor the ever-changing epidemiology of enteroviral infections also [
66].
Author Contributions
Conceptualization, C.P.M.; Methodology, C.P.M.; Validation, C.P.M., A.J. and J.H.; Formal Analysis, C.P.M., T.T., A.T. and J.H.; Investigation, C.P.M., A.J., L.B., H.H-W., N.A., B.C., G.C. and W.I.; Resources, C.P.M. and G.C.; Data Curation, C.P.M., A.J. and S.A.; Writing – Original Draft Preparation, C.P.M., A.J. and C.J.; Writing – Review & Editing, All authors; Visualization, C.P.M., A.T., J.H. and S.A.; Supervision, C.P.M.; Project Administration, C.P.M.; Funding Acquisition, C.P.M.