Article Reference

Article

Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank

BRITO, Francisco, et al.

Abstract

Platelet concentrates are frequently transfused to patients with reduced immunity. An exhaustive description of their viral content is needed to prevent unwanted infection.

Reference

BRITO, Francisco, et al. Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank. Vox Sanguinis, 2018

PMID : 30022500 DOI : 10.1111/vox.12695

Available at: http://archive-ouverte.unige.ch/unige:109659

Disclaimer: layout of this document may differ from the published version.

Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank

Francisco Brito,1,2 Samuel Cordey,3 Eric Delwart,4 Xutao Deng,4 Diderik Tirefort,5 Coralie Lemoine-Chaduc,6 Evgeny Zdobnov,1,2 Thomas Lecompte,5 Laurent Kaiser,3 Sophie Waldvogel-Abramowski5,6 & Olivier Preynat-Seauve5 1Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, Geneva, Switzerland 2Swiss Institute of Bioinformatics, Geneva, Switzerland 3Laboratory of Virology, University Hospitals of Geneva, Geneva, Switzerland 4Blood Systems Research Institute, San Francisco, CA, USA 5Department of Internal Medicine of Medical Specialties, Faculty of Medicine of Geneva, Geneva, Switzerland 6Blood Transfusion Center, University Hospitals of Geneva, Geneva, Switzerland

Background and objectives Platelet concentrates are frequently transfused to patients with reduced immunity. An exhaustive description of their viral content is needed to prevent unwanted infection. Material and methods To track viral sequences, a shotgun metagenomics approach was used on a bank of 300 platelets concentrates. Sequences were analysed through the diagnostics-oriented pipeline ezVIR. Results We only observed viruses commonly described in healthy individuals. Received: 12 February 2018, Conclusion Herein is reported the ﬁrst viral landscape of a platelet concentrates bank. revised 28 May 2018, accepted 25 June 2018, Key words: next-generation sequencing, platelet concentrates, transfusion-trans- published online 18 July 2018 missible infections.

9 6 Introduction donor’s plasma, and 0.23 10 residual leucocytes/unit. Four ml was derived from each concentrate before clini- Using metagenomics, we recently reported on the virome cal use. Samples were not pathogen-reduced. of red-blood-cell concentrates and fresh-frozen plasmas [1]. Platelet concentrates are frequently transfused to Nucleic acid extraction and Sequencing immunosuppressed patients. However, due to their limited availability for research, their viral landscape has not Extraction was made using the QIAamp Circulating been reported. To assess the risk of transfusing patho- Nucleic Acid Kit (Qiagen) without carrier RNA. Pools were genic viruses, we performed viral screening of 300 plate- made of 30 extracts each. Pool libraries were prepared as let concentrates manufactured at the blood transfusion previously described [1]. As positive controls, two centre of Geneva (Switzerland). libraries, one DNA (DNA B19V) and one RNA (RNA HRV14) were prepared from one spiked single concentrate 5 Material and methods with 10 copies/ml of Parvovirus B19 (B19V) and Human Rhinovirus 14 (HRV-14), respectively. Negative controls consisted of empty tubes submitted to the entire process. Platelet concentrates manufacturing Libraries were run on the HiSeq 2500, producing paired- Three hundred platelet concentrates were collected from end, 100 nt long reads. single donors in 2016 containing, on average, 39% of Library Analysis Correspondence: Olivier Preynat-Seauve, University Hospitals of Libraries were analysed with an updated version of ezVIR Geneva, Rue Gabrielle Perret Gentil 4. CH-1211 Geneva, Switzerland E-mail: [email protected] [2]. Non-human data were assembled using IDBA-UD, Brito and Cordey equally contributed to this study. and scaffolds were classiﬁed with DIAMOND, using NR as

601 602 F. Brito et al. the database. Cross-contamination was described as previ- global population and is known to be transmissible ously reported in [3]. Briefly, for each sequencing lane, a through transfusion [5, 6], with a tropism for bone mar- percentage of reads can be misattributed to other row, spleen and plasma [5]. While Herpesvirus 6 viraemia libraries. For each lane, we compared the libraries with has been described in the blood virome, the signal may most abundance of each virus, against the other libraries. also be due to HHV6 integrated in the genome [7]. While If the ratio was below 0.24%, they were considered as associated with skin flora, polyomavirus and papillo- contaminants. mavirus have also been reported in the blood of healthy individuals [7]. These observations suggest virus transmis- Results and discussion sion to the product from the donor’s blood. HHV6 reads were also detected in the negative control, mapping to a Twenty-four libraries were produced as follows: 10 DNA region common to several HHV6 strains (a repeat region pools, 10 RNA pools, two positive controls and two nega- in the first 3000 nt of the genome). As no hits for other tive controls (DNA and RNA). After removing low quality species were found for these reads, we discarded the pos- and complexity reads, DNA libraries were comprised of sibility of a reagent contaminant or read misclassification. an average of 91.2% human content and 8.8% non- It could be a case of cross-contamination from sample human content, while RNA libraries had an average of 10, although the low abundance of reads does not allow 89.5% human content and 10.5% non-human content. us to confirm it. Finally, known reagent contaminants are The spiked viruses–Parvovirus B19 (B19V) and Human found as follows: Parvo-like hybrid virus, Kadipiro virus Rhinovirus 14 (HRV-14)–were found with almost com- [8, 9] and Xenotropic murine leucemia-related virus [10]. plete coverage (99.99% and 99.98%, respectively). Herein is reported a novel insight into the viral land- Five virus families were identified (Fig. 1): Anelloviri- scape of a platelet concentrates bank. It contains less dae (Torque Teno Virus–TTV), Herpesviridae (Herpesvirus diversity of viral signatures than reported for the blood 6–HHV6), Papillomaviridae (Papillomavirus), Polyomaviri- virome, probably due to the plasma/leucocyte reduction dae (Polyomavirus and Merkel Cell Polyomavirus) and process applied to blood products manufacturing, and the Flaviviridae (human Pegivirus–HPgV). The percentage of high level of pooling in this study. Despite this, we were genome covered and number of reads for each virus are able to find several commensal viruses also present in shown in Table 1. These signals are consistent with stud- other blood products. Finding signatures of two DNA ies from other blood products, namely viruses reported to viruses in RNA libraries suggest a replication phase commonly circulate in the blood of healthy individuals: releasing RNA or incomplete DNase efficacy during TTV, Pegivirus, HHV6, Polyomavirus and Papillomavirus. library preparation. No uncommon viruses were found, TTV is detected in blood with a prevalence between 1.9% unlike our previous analysis in red blood cells and plasma and 62% and a tropism for peripheral mononuclear cells, [1], where we found an Astrovirus MLB2 linked to liver and bone marrow [4]. Pegivirus infects 1/6 of the meningitis in immunocompromised patients [11]. As

Lane 1 Lane 2Lane 3 Lane 4 Lane 5 Lane 6

Torque-teno virus Read Rhinovirus abundance Herpesvirus 6A 0 Papillomavirus 1 – 2 <10 Parvovirus <10² Merkel cell polyomavirus <10³ Polyomavirus <104 Pegivirus 1 <105 6 Kadipirovirus <10 <107 Parvo−like hybrid virus <108 Xenotropic MuLV−related virus >108

ve 4 ve V Cross-talk Contaminants Found Viruses ti 1 ti 9 a V a 1 RNA1RNA2RNA3RNA4RNA5RNA6RNA7RNA8RNA9 g R DNA1DNA2DNA3DNA4DNA5DNA6DNA7DNA8DNA9 g B RNA10e H DNA10e A N A N N A N A D N R N R D Library

Fig. 1 Viral signatures in each individual pool sorted by sequencing lane and sequencing type. The dotted libraries represent cross-talk contaminations.

Table 1 Quantitative values of virus signals found by ezVIR

Library Virus family Genome name ID % covered Genome length Total mapped reads

DNA 1 None None DNA 2 Herpesvirus 6A Human herpesvirus 6A AJ KP257584.1 0.54 156 714 16 DNA 3 TT virus Torque teno virus 1 NC 002076.2 5.19 3852 3 DNA 4 None None DNA 5 None None DNA 6 None None DNA 7 TT virus Torque teno midi virus 2 MD2-013 AB290919.1 11.96 3253 14 DNA 8 Polyomavirus Polyomavirus HPyV6 607b HM011561.1 2.42 4926 2 Papillomavirus Human papillomavirus type 20 U31778.1 1.33 7757 2 DNA 9 Merkel cell polyomavirus Merkel cell polyomavirus MCC350 EU375803.1 6.48 5387 4 TT virus Torque teno virus 1 NC 002076.2 2.60 3852 2 DNA 10 Herpesvirus 6A Human herpesvirus 6A AJ KP257584.1 0.55 156 714 12 DNA negative Herpesvirus 6A Human herpesvirus 6A GS KJ123690.1 0.06 156 864 3 DNA B19V Parvovirus Human parvovirus B19 NC 000883.2 99.98 5596 65 895 350 RNA 1 Merkel cell polyomavirus Merkel cell polyomavirus MCC350 EU375803.1 3.71 5387 2 RNA 2 None None RNA 3 None None RNA 4 Papillomavirus Human papillomavirus type 107 EF422221.1 1.32 7562 4 RNA 5 None None RNA 6 Pegivirus 1 Hepatitis GB virus C GT110 D90600.1 96.66 9395 32 787 RNA 7 Pegivirus 1 Hepatitis GB virus C GT110 D90600.1 97.79 9395 32 322 RNA 8 None None RNA 9 Papillomavirus Human papillomavirus type 107 EF422221.1 1.32 7562 11 RNA 10 Pegivirus 1 Hepatitis G virus strain HGV AF081782.1 53.73 9373 485 RNA negative None None RNA HRV 14 Rhinovirus Human rhinovirus type 14 K02121.1 99.99 7212 102 745 995 Papillomavirus Human papillomavirus type 18 X05015.1 29.50 7857 175

generally observed in high-throughput sequencing, Acknowledgements unspecific background signal was systematically present and must be carefully identified and removed. This is Production and quality control staff of the blood transfu- achieved by controlling for specific reagents, using dou- sion centre of Geneva, staff of the genomic core facility, ble indexing, and complementing the analysis with robust faculty of medicine of Geneva, for HTS. molecular methods, respectively [3, 8–10]. Thus, a metagenomic approach offers an attractive option for the Funding exhaustive screening of platelet concentrate banks, as it allows for the detection of viruses which are not part of Dubois Ferriere Dinu Lipatti Foundation, unrestricted standard diagnostics, and also can lead to follow-up asso- grant from AstraZeneca (OPS), National Heart, Lung, and ciation studies in larger platelet banks and/or defined Blood Institute (ED, No. R01 HL105770), IGE3 PhD Stu- donor populations [11, 12]. dent Award (FB).

References

1 Lau P, Cordey S, Brito F, et al.: with a user-friendly representation of 4 Spandole S, Cimponeriu D, Berca LM, Metagenomics analysis of red blood bioinformatics analysis: a pilot study. et al.: Human anelloviruses: an update cell and fresh-frozen plasma units. J Clin Microbiol 2014; 52:3351–3361 of molecular, epidemiological and Transfusion 2017; 57:1787–1800 3 Wright ES, Vetsigian KH: Quality ﬁl- clinical aspects. Arch Virol 2015; 2 Petty TJ, Cordey S, Padioleau I, et al.: tering of Illumina index reads miti- 160:893–908 Comprehensive human virus screening gates sample cross-talk. BMC Genom 5 Bailey AL, Lauck M, Mohns M, et al.: using high-throughput sequencing 2016; 17:876 Durable sequence stability and bone

marrow tropism in a macaque model humans. Belshaw R, ed. PLoS Pathog 10 Simmons G, Glynn SA, Komaroff AL, of human pegivirus infection HHS 2017; 13:e1006292 et al.: Failure to conﬁrm XMRV/MLVs Public Access Together, these results 8 Naccache SN, Greninger AL, Lee D, in the blood of patients with chronic reconcile several paradoxical observa- et al.: The Perils of Pathogen fatigue syndrome: a multi-laboratory tions from cross-sectional analyses of Discovery: origin of a Novel study. Science 2011; 334:814–817 HPgV in humans and provide an ani- Parvovirus-Like Hybrid Genome 11 Cordey S, Vu D-L, Schibler M, et al.: mal model for studying pegivirus biol- Traced to Nucleic Acid Extraction Astrovirus MLB2, a New Gastroenteric ogy. Sci Transl Med 2015; 7:305–144 Spin Columns. J Virol 2013; Virus Associated with Meningitis and 6 Bernardin F, Operskalski E, Busch M, 87:11966–11977 Disseminated Infection. Emerg Infect et al.: Transfusion transmission of 9 Ngoi CN, Siqueira J, Li L, et al.: Corri- Dis 2016; 22:846–853 highly prevalent commensal human gendum: the plasma virome of febrile 12 Wilson MR, Fedewa G, Stenglein MD, viruses. Transfusion 2010; 50:2474– adult Kenyans shows frequent par- et al. Multiplexed metagenomic deep 2483 vovirus B19 infections and a novel sequencing to analyze the composition 7 Moustafa A, Xie C, Kirkness E, et al.: arbovirus (Kadipiro virus). J Gen Virol of high-priority pathogen reagents. Chia The blood DNA virome in 8,000 2017; 98:517 N, ed. mSystems. 2016;1:e00058. 16