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Chan Zuckerberg Biohub
5th Anniversary

Learn more about our first five years of innovation and discovery, and watch highlights from our scientific symposium, featuring keynotes from NIH Director Francis Collins and others.

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RAPID RESPONSE TEAM

Welcome to the Rapid Response Team

The CZ Biohub Rapid Response Team provides resources for training, tools, and technologies to help support sustainable scientific platforms in laboratories around the world.

Our Mission

We are working to cultivate global equity in basic and translational research for improved surveillance and response to emerging infectious diseases within underserved geographies.

Malagasy researchers learning next generation sequencing techniques at the CZ Biohub as part of a collaboration with the Rapid Response Team.

Rapid Response Scientist Vida Ahyong visiting researchers in their lab in Cambodia and reviewing next-generation sequencing protocols.

Kenyan researchers at CZ Biohub in San Francisco. The team spent six weeks learning next-generation sequencing skills through a collaboration with the Rapid Response Team.

Bangladeshi scientists with their lab’s first benchtop sequencer, which enabled their research team to sequence patient samples and analyze the resulting data within their home country.

Our Resources

 

The Rapid Response Team provides metagenomics (mNGS) training and support to groups all over the world. Here you will find mNGS protocols and training materials that were developed in collaboration with the Genomics Team at CZ Biohub and the IDseq team at the Chan Zuckerberg Initiative.

Lab Protocols

  • Metagenomic next-generation sequencing (mNGS) protocols. LEARN MORE
  • SARS-CoV-2 metagenomic sequencing by spiked primer enrichment (MSSPE), library prep protocol. LEARN MORE
  • SARS-CoV-2 ARTIC sequencing using Illumina, library prep protocol. LEARN MORE

Training Materials

A. Metagenomic Sequencing
B. Enrichment/Depletion Methods for Sequencing
C. Additional Material

Publications

Rapid deployment of SARS-CoV-2 testing: the CLIAHUB.

Crawford ED, Acosta I, Ahyong V, et al. PLoS Pathog. 2020 Oct 28;16(10):e1008966. doi: 10.1371/journal.ppat.1008966. eCollection 2020 Oct. PMID: 33112933

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by RT-PCR.

Vanaerschot M, Mann SA, Webber JT, Kamm J, Bell SM, Bell J, Hong SN, Nguyen MP, Chan LY, Bhatt KD, Tan M, Detweiler AM, Espinosa A, Wu W, Batson J, Dynerman D; CLIAHUB Consortium, Wadford DA, Puschnik AS, Neff N, Ahyong V, Miller S, Ayscue P, Tato CM, Paul S, Kistler A, DeRisi JL, Crawford ED. J Clin Microbiol. 2020 Dec 17:59(1):e02369-20. doi: 10.1128/JCM.02369-20. Online ahead of print. PMID: 33067272

Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection.

Elledge SK, Zhou XX, Byrnes JR, Martinko AJ, Lui I, Pance K, Lim SA, Glasgow JE, Glasgow AA, Turcios K, Iyer N, Torres L, Peluso MJ, Henrich TJ, Wang TT, Tato CM, Leung KK, Greenhouse B, Wells JA. medRxiv. 2020 Aug 21:2020.08.17.20176925. doi: 10.1101/2020.08.17.20176925. Preprint. PMID: 32839788

IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.

Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, Kislyuk A, Lin MF, Mariano M, Morse T, Reynoso LV, Cruz DR, Sheu J, Tang J, Wang J, Zhang MA, Zhong E, Ahyong V, Lay S, Chea S, Bohl JA, Manning JE, Tato CM, DeRisi JL. Gigascience. 2020 Oct 15;9(10):giaa111. doi: 10.1093/gigascience/giaa111. PMID: 33057676; PMCID: PMC7566497.

Co-occurrence of campylobacter species in children from Eastern Ethiopia, and their association with environmental enteric dysfunction, diarrhea, and host microbiome.

Terefe Y, Deblais L, Ghanem M, Helmy YA, Mummed B, Chen D, Singh N, Ahyong V, Kalantar K, Yimer G, Yousuf Hassen J, Mohammed A, McKune SL, Manary MJ, Ordiz MI, Gebreyes W, Havelaar AH, Rajashekara G. Front Public Health. 2020 Apr 15;8:99. doi: 10.3389/fpubh.2020.00099. eCollection 2020. PMID: 32351922

Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive chikungunya virus outbreak and other unrealized pathogens.

Saha S, Ramesh A, Kalantar K, Malaker R, Hasanuzzaman M, Khan LM, Mayday MY, Sajib MSI, Li LM, Langelier C, Rahman H, Crawford ED, Tato CM, Islam M, Juan YF, de Bourcy C, Dimitrov B, Wang J, Tang J, Sheu J, Egger R, De Carvalho TR, Wilson MR, Saha SK, DeRisi JL. mBio. 2019 Dec 17;10(6):e02877-19. doi: 10.1128/mBio.02877-19. PMID: 31848287; PMCID: PMC6918088.

Investigating transfusion-related sepsis using culture-independent metagenomic sequencing.

Crawford E, Kamm J, Miller S, Li LM, Caldera S, Lyden A, Yokoe D, Nichols A, Tran NK, Barnard SE, Conner PM, Nambiar A, Zinter MS, Moayeri M, Serpa PH, Prince BC, Quan J, Sit R, Tan M, Phelps M, Derisi JL, Tato CM, Langelier C. Clin Infect Dis. 2020 Aug 22;71(5):1179-1185. doi: 10.1093/cid/ciz960. PMID: 31563940; PMCID: PMC7442849.

Complete genome sequence of a novel coronavirus (SARS-CoV-2) isolate from Bangladesh.

Saha S, Malaker R, Sajib MSI, Hasanuzzaman M, Rahman H, Ahmed ZB, Islam MS, Islam M, Hooda Y, Ahyong V, Vanaerschot M, Batson J, Hao S, Kamm J, Kistler A, Tato CM, DeRisi JL, Saha SK. Microbiol Resour Announc. 2020 Jun 11;9(24):e00568-20. doi: 10.1128/MRA.00568-20. PMID: 32527780; PMCID: PMC7291105.

Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia.

Manning JE, Bohl JA, Lay S, Chea S, Sovann L, Sengdoeurn Y, Heng S, Vuthy C, Kalantar K, Ahyong V, Tan M, Sheu J, Tato CM, DeRisi JL, Baril L, Duong V, Dussart P, Karlsson EA. bioRxiv [Preprint]. 2020 Mar 5:2020.03.02.968818. doi: 10.1101/2020.03.02.968818. PMID: 32511296; PMCID: PMC7217139.

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Schubert RD, Hawes IA, Ramachandran PS, Ramesh A, Crawford ED, Pak JE, Wu W, Cheung CK, O’Donovan BD, Tato CM, Lyden A, Tan M, Sit R, Sowa GA, Sample HA, Zorn KC, Banerji D, Khan LM, Bove R, Hauser SL, Gelfand AA, Johnson-Kerner BL, Nash K, Krishnamoorthy KS, Chitnis T, Ding JZ, McMillan HJ, Chiu CY, Briggs B, Glaser CA, Yen C, Chu V, Wadford DA, Dominguez SR, Ng TFF, Marine RL, Lopez AS, Nix WA, Soldatos A, Gorman MP, Benson L, Messacar K, Konopka-Anstadt JL, Oberste MS, DeRisi JL, Wilson MR. Nat Med. 2019 Nov;25(11):1748-1752. doi: 10.1038/s41591-019-0613-1. Epub 2019 Oct 21. PMID: 31636453

Team

News

Partner Highlight: Building up their pipeline!

December 22, 2020

Congratulations to the lab team at the Child Health Research Foundation (CHRF) in Dhaka, Bangladesh for receiving their brand new sequencer!

The team at CHRF was one of the first lab groups to come to CZ Biohub in San Francisco for hands-on training in metagenomic sequencing (mNGS). Since then, we have seen CHRF soar to new heights as they put mNGS to work to help address a wide variety of public health, questions from identifying the underlying causes of pediatric meningitis, to performing genomic epidemiology during an outbreak of Dengue virus. CHRF also became the first group in Bangladesh to sequence whole genomes of SARS-CoV-2 early on in the pandemic – using only a small portable sequencer! Keep up the good work!

Stay calm and keep training!

December 16, 2020

We were thrown a curve ball in 2020, but didn’t let the pandemic stop us from our training activities. We participated in a number of online courses this year – and one particular highlight was virtually traveling to eastern Africa to conduct a course in genomics and bioinformatics. During our week-long course CZ Biohub Rapid Response teamed up with colleagues at the Chan Zuckerberg Initiative to introduce the use of next-generation sequencing and analytical tools for studying the cause, source, and dynamics of infectious disease, and for utilization in disease outbreak response efforts.

This class was part of the Global One Health Summer Institute, which is organized and hosted by our collaborators in the Global One Health Initiative at The Ohio State University and includes a number of courses run by a large variety of institutions from around the world. This year’s Summer Institute reached 1,200 trainees from 43 countries!