Title Phylogenetic characterization of rhinoviruses from infants in Sarlahi, Nepal.
Author Kuypers, Jane; Perchetti, Garrett A; Chu, Helen Y; Newman, Kira L; Katz, Joanne; Khatry, Subarna K; LeClerq, Steven C; Jerome, Keith R; Tielsch, James M; Englund, Janet A
Journal J Med Virol Publication Year/Month 2019-Dec
PMID 31389049 PMCID PMC6800797
Affiliation + expend 1.Department of Laboratory Medicine, University of Washington, Seattle, Washington.

PROBLEM: Rhinoviruses (RVs), the most common causes of acute respiratory infections in young children and infants, are highly diverse genetically. OBJECTIVE: To characterize the RV types detected with respiratory illness episodes in infants in Nepal. STUDY METHODS: Infants born to women enrolled in a randomized trial of maternal influenza immunization in rural, southern Nepal were followed with household-based weekly surveillance until 180 days of age. Infants with respiratory symptoms had nasal swabs tested for twelve respiratory viruses. A subset with RV alone was selected for sequencing of the VP4/2 gene to identify RV types. RESULTS: Among 547 RV-only positive illnesses detected from December 2012 to April 2014, 285 samples (52%) were sequenced. RV-A, B, and C species were detected in 193 (68%), 18 (6%), and 74 (26%) specimens, respectively. A total of 94 unique types were identified from the sequenced samples, including 52 RV-A, 11 RV-B, and 31 RV-C. Multiple species and types circulated simultaneously throughout the study period. No seasonality was observed. The median ages at illness onset were 88, 104, and 88 days for RV-A, B, and C, respectively. The median polymerase chain reaction cycle threshold values did not differ between RV species. No differences between RV species were observed for reported respiratory symptoms, including pneumonia, or for medical care-seeking. CONCLUSIONS: Among very young, symptomatic infants in rural Nepal, all three species and many types of RV were identified; RV-A was detected most frequently. There was no association between RV species and disease severity.

StrainID RV Species Serotype Length(nt) Country Year Strain Name
CNM01775 C None 431 Nepal 2013 PS6367
CNM01780 C None 409 Nepal 2012 PS4534
CNM01785 C None 441 Nepal 2013 PS5375
CNM01790 C None 439 Nepal 2013 PS4903
CNM01795 C None 441 Nepal 2013 PS5822
CNM01800 C None 441 Nepal 2013 PS5948
CNM01805 C None 441 Nepal 2013 PS6424
CNM01810 C None 441 Nepal 2013 PS6293
CNM01815 C None 438 Nepal 2014 PS6611
CNM01820 C None 441 Nepal 2013 PS4782
CNM01825 C None 441 Nepal 2012 PS4690
CNM01830 C None 441 Nepal 2012 PS4570
CNM01835 C None 441 Nepal 2013 PS4725
CNM01840 C None 429 Nepal 2013 PS4767
CNM01845 C None 432 Nepal 2013 PS6427
CNM01850 C None 441 Nepal 2013 PS6114
CNP01777 C None 439 Nepal 2013 PS6373
CNP01782 C None 441 Nepal 2012 PS4591
CNP01787 C None 392 Nepal 2013 PS4755
CNP01792 C None 441 Nepal 2013 PS4927
CNP01797 C None 441 Nepal 2013 PS6010
CNP01802 C None 441 Nepal 2012 PS4673
CNP01807 C None 441 Nepal 2013 PS4873
CNP01812 C None 441 Nepal 2013 PS5533
CNP01817 C None 441 Nepal 2012 PS4620
CNP01822 C None 441 Nepal 2014 PS6521
CNP01827 C None 441 Nepal 2013 PS4807
CNP01832 C None 441 Nepal 2013 PS5676
CNP01837 C None 441 Nepal 2014 PS6522
CNP01842 C None 413 Nepal 2013 PS4718
CNP01847 C None 430 Nepal 2013 PS6194
CNS01773 C None 404 Nepal 2013 PS6381
CNS01778 C None 431 Nepal 2013 PS6268
CNS01783 C None 441 Nepal 2013 PS5617
CNS01788 C None 441 Nepal 2012 PS4555
CNS01793 C None 442 Nepal 2013 PS4945
CNS01798 C None 441 Nepal 2013 PS6418
CNS01803 C None 441 Nepal 2012 PS4602
CNS01808 C None 431 Nepal 2012 PS4558
CNS01813 C None 441 Nepal 2012 PS4579
CNS01818 C None 441 Nepal 2013 PS4864
CNS01823 C None 441 Nepal 2013 PS6201
CNS01828 C None 441 Nepal 2013 PS4762
CNS01833 C None 441 Nepal 2013 PS5766
CNS01838 C None 431 Nepal 2013 PS6456
CNS01843 C None 387 Nepal 2012 PS4638
CNS01848 C None 423 Nepal 2013 PS6092
CNZ01776 C None 348 Nepal 2013 PS4940
CNZ01781 C None 441 Nepal 2014 PS6548
CNZ01786 C None 441 Nepal 2013 PS4857
CNZ01791 C None 441 Nepal 2012 PS4693
CNZ01796 C None 441 Nepal 2013 PS5111
CNZ01801 C None 441 Nepal 2013 PS5619
CNZ01806 C None 442 Nepal 2012 PS4601
CNZ01811 C None 441 Nepal 2013 PS6475
CNZ01816 C None 440 Nepal 2012 PS4561
CNZ01821 C None 441 Nepal 2013 PS4830
CNZ01826 C None 441 Nepal 2013 PS4730
CNZ01831 C None 441 Nepal 2013 PS6361
CNZ01836 C None 441 Nepal 2012 PS4563
CNZ01841 C None 426 Nepal 2012 PS4577
CNZ01846 C None 437 Nepal 2013 PS5267
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