Replication Data for: Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024 (doi:10.7910/DVN/DV9DCM)

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Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Part 5: Other Study-Related Materials
Entire Codebook

Replication Data for: Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024

doi:10.7910/DVN/DV9DCM

Harvard Dataverse

2025-12-01

3

Okanda, Dorcas; Oduor Odoyo, Samuel; Kiprono, Hillary; Katama, Esther Nyadzua; Maina, Grace; Mutunga, martin; Nyiro, Joyce; Agoti, Charles Nyaigoti; Githinji, George, 2025, "Replication Data for: Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024", https://doi.org/10.7910/DVN/DV9DCM, Harvard Dataverse, V3, UNF:6:4zgBEMrKgGr4NfRqXf+2aA== [fileUNF]

Replication Data for: Molecular Epidemiology of Human Metapneumovirus in Kilifi, Coastal Kenya, 2016-2017 and 2021-2024

doi:10.7910/DVN/DV9DCM

Okanda, Dorcas (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Oduor Odoyo, Samuel (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Kiprono, Hillary (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Katama, Esther Nyadzua (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Maina, Grace (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Mutunga, martin (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Nyiro, Joyce (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Agoti, Charles Nyaigoti (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Githinji, George (KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya)

Harvard Dataverse

Okanda, Dorcas

Githinji, George

The Data Governance Committee

Okanda, Dorcas

2025-12-01

https://doi.org/10.7910/DVN/DV9DCM

Medicine, Health and Life Sciences, hMPV, A2c-111-dup, whole genome sequencing, Oxford Nanopore Technologies, Kilifi, Kenya

<p>This is a replication dataset for the manuscript titled: "<strong><i>Molecular Epidemiology of Human Metapneumovirus in Coastal Kenya (2016-2024)</i></strong>."</p> <p>The datasets are part of ongoing surveillance either in the outpatient and community within the KHDSS in coastal Kenya. Dataset1 shows individual case data with demographic characteristics (age, sex etc.) and clinical characteristics (including symptoms status, fever, cough among others). Dataset2 contains individual case data with genomic characteristics (variant, nextclade lineage and genome coverage).</p>

Open Access

<strong>The datasets will become open for download once the corresponding manuscript is published.</strong>

The datasets will become open for download once the corresponding manuscript is published.

<a href="http://creativecommons.org/licenses/by/4.0">CC BY 4.0</a>

• Number of cases: 186

• No. of variables per record: 69

• Type of File: text/tab-separated-values

UNF:6:dIzatUNk17UdU2on8fhYgA==

• Number of cases: 52

• No. of variables per record: 6

• Type of File: text/tab-separated-values

UNF:6:nokFy23xT2G8w9WKhCJpOA==

• study_serial - study_serial
• id - id
• ID_GRP - ID_GRP
• date_collect - date_collect
• hmpv_n - hmpv_n
• hmpv_n_bin - hmpv_n_bin
• sex - sex
• location - location
• age - age
• cough - cough
• headache - headache
• chills - chills
• running_nose - running_nose
• fatigue - fatigue
• sore_throat - sore_throat
• wheezing - wheezing
• vomiting - vomiting
• nausea - nausea
• diarrhea - diarrhea
• myalgia - myalgia
• chestpains - chestpains
• diff_breath - diff_breath
• fever - fever
• joint_pains - joint_pains
• loss_taste - loss_taste
• nasal_congestion - nasal_congestion
• lose_appetite - lose_appetite
• temp - temp
• nasal_discharge - nasal_discharge
• nasal_flaring - nasal_flaring
• indrawing - indrawing
• crackles - crackles
• wheezes - wheezes
• feed_unable - feed_unable
• head_nodding - head_nodding
• cyanosis - cyanosis
• jointpains - jointpains
• bodymalaise - bodymalaise
• Abdominal_pains - Abdominal_pains
• Lack_of_appetite - Lack_of_appetite
• Loss_of_smell - Loss_of_smell
• chest_pain - chest_pain
• Nausea - Nausea
• joint_pain - joint_pain
• Back_pain - Back_pain
• Body_ache - Body_ache
• Epigastric_pain - Epigastric_pain
• Sneezing - Sneezing
• Dizziness - Dizziness
• weight - weight
• height - height
• muac - muac
• head_circum - head_circum
• oxygen_saturation - oxygen_saturation
• heart_rate - heart_rate
• axillary_temp - axillary_temp
• resp_rate - resp_rate
• nasaldischarge - nasaldischarge
• breathing_difficulty - breathing_difficulty
• nasal_flare - nasal_flare
• wheeze - wheeze
• unable_to_feed - unable_to_feed
• headnod - headnod
• unable_talk - unable_talk
• conscious_level - conscious_level
• tag - tag
• period - period
• age_grp - age_grp
• Facility1 - Facility1
• study_serial - study_serial
• strain_id - strain_id
• collection_date - collection_date
• status - status
• genotype - genotype
• year - year

f13405925 Location:

Summary Statistics: StDev 2596.0600218622253; Valid 186.0; Mean 5631.360215053764; Min. 1040.0; Max. 9977.0;

Variable Format: numeric

Notes: UNF:6:ixoqR/8O8a8JzhmmTzV+sg==

f13405925 Location:

Variable Format: character

Notes: UNF:6:sypFjBDa/ST+30R6w/BSpw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:vv4d+T7r7uu/Jx+orbqkUQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:2NwEv2nFg/dT/KnvbSNi3A==

f13405925 Location:

Summary Statistics: StDev 3.4941361641963886; Mean 28.6488988425142; Max. 34.9773826599121; Min. 15.97802734375; Valid 186.0;

Variable Format: numeric

Notes: UNF:6:0OZ1tmUU2mosRx2WDdzIdA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:+ve12bPCwPCHK3K5/x5H/g==

f13405925 Location:

Variable Format: character

Notes: UNF:6:+jokiYi4GSkA+ieFnLC2uA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:r72g2F6qiw10g04vEVIKNw==

f13405925 Location:

Summary Statistics: Max. 59.0; StDev 10.467731793123273; Min. 0.0; Valid 186.0; Mean 6.85483870967742

Variable Format: numeric

Notes: UNF:6:kX3VKnSSzaVT6HcKPBHsEQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:nhbMC057KbyDJ+Pzrx7Z8A==

f13405925 Location:

Variable Format: character

Notes: UNF:6:LZ10UE9p6x0YMUPMmM3SDg==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:m1wi80dUojMYTrHQ+ygdhA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:uzpQLTCj1wtn0z1Ql8PlIg==

f13405925 Location:

Variable Format: character

Notes: UNF:6:dvk1tqsvwQiIjj6fxDK2DA==

f13405925 Location:

Variable Format: character

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f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:TR6yilBum18i5tBczyLCuA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:lncfSMmh/1ZO+BMqk43hbA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:OjYTXq0lHMx5Kj+F/X4eZA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:32A5amhwUBFTmzHk3Dx1iA==

f13405925 Location:

Summary Statistics: Min. 35.0; Mean 35.92702702702703; Valid 37.0; StDev 0.6167336218825441; Max. 38.1

Variable Format: numeric

Notes: UNF:6:EIBLWw+e6udv20ohlrfqwg==

f13405925 Location:

Variable Format: character

Notes: UNF:6:QJl/i3FDJtSwQ8d3DRKodg==

f13405925 Location:

Variable Format: character

Notes: UNF:6:gCig3BGkK2JrfLXHJhM4TQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:MeXKYMikT5BDDpeCFuiXWA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:6mkx7u/p9598UJ1HF+QeJQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:icwdfYZ2VgRRgTuXYt5Yfg==

f13405925 Location:

Variable Format: character

Notes: UNF:6:GMZCg1WqISfw6Z9YbIIt1g==

f13405925 Location:

Variable Format: character

Notes: UNF:6:aeMRnrTLUDq+/Uu7yfWeEw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:9bZuJKYYTVeQ0XfhAtdstQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:jHy2PXECoMYAlkuWi4OUoA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:k0IzU42CdV42wT004XIWWA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:Il1+fdqVL1u6ZVLE5be4ZA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:Ois4H+Q4oqEqx3v/o9mB/g==

f13405925 Location:

Variable Format: character

Notes: UNF:6:aeMRnrTLUDq+/Uu7yfWeEw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:KFhG6xBK53jr4C09LlhqAw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:aeMRnrTLUDq+/Uu7yfWeEw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:aeMRnrTLUDq+/Uu7yfWeEw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:7yUTfUAlPSzrzRsRIAG6JQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:aeMRnrTLUDq+/Uu7yfWeEw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:aeMRnrTLUDq+/Uu7yfWeEw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:aeMRnrTLUDq+/Uu7yfWeEw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:ZMJ7Ns01ExHXfebhGS2NsA==

f13405925 Location:

Summary Statistics: Mean 12.241860446264578; StDev 9.2310022963265; Min. 4.30000019073486; Valid 86.0; Max. 85.0

Variable Format: numeric

Notes: UNF:6:Lx8IGLTqG2lfvut+wJNagQ==

f13405925 Location:

Summary Statistics: StDev 18.751950300401074; Max. 140.5; Mean 82.60116266649823; Min. 45.0; Valid 86.0

Variable Format: numeric

Notes: UNF:6:7y88+mmQjljHgu/GQUzGHg==

f13405925 Location:

Summary Statistics: StDev 4.151631443940485; Max. 50.0; Valid 86.0; Min. 6.0; Mean 15.025581370952514

Variable Format: numeric

Notes: UNF:6:K/PGddtaiJ9YAkO4p6Ct/w==

f13405925 Location:

Summary Statistics: Valid 87.0; StDev 4.2652255849126535; Mean 47.23793099940508; Max. 69.0; Min. 35.0;

Variable Format: numeric

Notes: UNF:6:YgpDCUuADRLjqWnvcZgJ2g==

f13405925 Location:

Summary Statistics: Mean 98.46315789473684; Valid 95.0; Min. 83.0; Max. 100.0; StDev 2.4048290349981207

Variable Format: numeric

Notes: UNF:6:kftHJ2AuxleNOPjuZfV5vQ==

f13405925 Location:

Summary Statistics: Max. 100.0; StDev 27.508532728961328; Valid 95.0; Mean 24.06315789473684; Min. 10.0

Variable Format: numeric

Notes: UNF:6:yfchqs/orBxGEP0dU/ctLQ==

f13405925 Location:

Summary Statistics: Min. 35.0; Max. 39.0; StDev 0.8028504648942818; Mean 36.61052631578947; Valid 95.0

Variable Format: numeric

Notes: UNF:6:QAka78AT6XHS2yXNZ3Xn+g==

f13405925 Location:

Summary Statistics: Min. 21.0; Max. 82.0; Valid 95.0; Mean 36.38947368421053; StDev 9.775452034867866

Variable Format: numeric

Notes: UNF:6:gQKzmRIw/b5RU3P7aYHGsw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:odQThs+MEE2IrA97l8HeOw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:OYNrbLRlgEnA5FwT6GZ5PA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:dZvBZc9p9ZIsvCrX9ZRkOw==

f13405925 Location:

Variable Format: character

Notes: UNF:6:H0lfzASTXdJpbvqGzkXSlQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:CqY8Mo6EgErmQLsRMNuxuQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:CqY8Mo6EgErmQLsRMNuxuQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:H0lfzASTXdJpbvqGzkXSlQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:WA9tb4IZIN86g8Uw4ye9iQ==

f13405925 Location:

Summary Statistics: Max. 1.0; StDev 0.0; Valid 186.0; Mean 1.0; Min. 1.0;

Variable Format: numeric

Notes: UNF:6:WiAOpd9OspJZLLQ5PPgFAw==

f13405925 Location:

Summary Statistics: Mean 2018.8978494623657; Valid 186.0; StDev 3.057166272949382; Max. 2024.0; Min. 2015.0;

Variable Format: numeric

Notes: UNF:6:53LXNVK9VqwnpCDo98DGwQ==

f13405925 Location:

Variable Format: character

Notes: UNF:6:sklQKtNLHm6mZtE/gBOQUA==

f13405925 Location:

Variable Format: character

Notes: UNF:6:zbN4c/DQUaTvEyHUZvDKvg==

f13405924 Location:

Summary Statistics: Valid 52.0; StDev 2434.0036923470293; Max. 9943.0; Mean 5559.423076923077; Min. 1040.0

Variable Format: numeric

Notes: UNF:6:XMAdgH4et4sOhxgRCH4S4Q==

f13405924 Location:

Variable Format: character

Notes: UNF:6:t0uL4lHmK4DvnoV+OoxGvg==

f13405924 Location:

Variable Format: character

Notes: UNF:6:SK8TuybpHescj74ejyXT1w==

f13405924 Location:

Variable Format: character

Notes: UNF:6:EyIZG/s4GRRYi+hC/HfHBQ==

f13405924 Location:

Variable Format: character

Notes: UNF:6:8fVoNaxSPSz/yQV0/VMGLg==

f13405924 Location:

Summary Statistics: Min. 2015.0; StDev 3.0631242245594525; Max. 2023.0; Mean 2019.9038461538462; Valid 52.0;

Variable Format: numeric

Notes: UNF:6:UlEtKu/H7Vwtrmaj3iYKMw==

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HMPV_Data_Dictionary_DorcasOakanda.pdf

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HMPV_Data_Readme_DorcasOakanda.txt

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