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The Freed Lab focuses on using cutting edge molecular tools to address a wide range of questions in microbial genetics. We are interested in a range of diverse research topics that relate to evolution, ecology, and microbiology. Our lab is located at the School of Biological Sciences at the University of Auckland. Nikki also runs Auckland Genomics, the genomics facility there.
The Freed Lab focuses on using cutting edge molecular tools to address a wide range of questions in microbial genetics. We are interested in a range of diverse research topics that relate to evolution, ecology, and microbiology. Our lab is located at the School of Biological Sciences at the University of Auckland. Nikki also runs Auckland Genomics, the genomics facility there.
News!! Marsden success and COVID 19 genome sequencing
News!! Marsden success and COVID 19 genome sequencing
Nov 2021:
Nikki was featured on the Royal Society's website for World World Antimicrobial Awareness Week
https://www.royalsociety.org.nz/news/waaw-dr-nikki-freed/
Oct 2021:
We are very excited to see that our COVID-19 "Midnight" method has been scaled up and is now being distributed by Oxford nanopore at a range of throughput (from 1 to 5000 samples) for rapidly and inexpensively ($9.55 per genome) sequencing the genome of SARS-CoV2.
July 2021:
Our COVID-19 "Midnight" primer pool has been distributed by IDT to >180 organizations across 35 countries, totalling more than 300,000 reactions. These numbers do not include when these primers are used for PacBio sequencing, or when labs order them and mix them manually.
It the primary primer set used by PacBio and is now one of two sets used by Oxford Nanopore for sequencing the genome of SARS-CoV2.
It can be used with Illumina sequencing as well, see protocols from Seqwell and IDT
Jan 2021:
New Preprint on tracking the spread of the SARS-CoV2 variant B.1.1.7 and B.1.351/501Y.V2
Nov 2020:
We were granted $300,000 to investigate the evolution of antibiotic resistance by Te Pūtea Rangahau a Marsden, the Marsden Fund, from the Royal Society of New Zealand Te Apārangi (November 2020).
Official site: https://www.royalsociety.org.nz/what-we-do/funds-and-opportunities/marsden/awarded-grants/marsden-fund-awards-2020/
Link: project proposal
We contributed to this clickable summary about the August COVID-19 Auckland outbreak on Nextstrain.org. Well worth looking and clicking around on.
https://nextstrain.org/community/narratives/ESR-NZ/GenomicsNarrativeSARSCoV2/2020-10-01
August 2020:
We "sprung into action" to use our method to sequence the genomes of the index cases and initial community isolates during the August 2020 Auckland outbreak. From nasal swab sample to polished genomes in 8 hours.
July 2020:
Olin Silander and Nikki Freed were live on Radio New Zealand to talk about COVID-19 work (~20 minutes) https://www.rnz.co.nz/national/programmes/nights/audio/2018756141/sequencing-the-genome-of-covid-19
July 2020: Massey University did a short interview on the COVID-19 work.
July 2020: Our paper on the faster, cheaper, and more robust method for sequencing the virus that causes COVID-19 is here https://academic.oup.com/biomethods/article/5/1/bpaa014/5873518
Press Release from Massey on COVID work: https://www.massey.ac.nz/massey/about-massey/news/article.cfm?mnarticle_uuid=A5D86772-95AD-4816-A282-389FBB164B6C
April 2020: Press release on the COVID-19 funding award from Ministry of Health and the Health Research Council (~$165,000 NZD) : https://www.massey.ac.nz/massey/about-massey/news/article.cfm?mnarticle_uuid=68840EC8-29F3-4FA8-9238-08CB590F5669
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