Efrem Lim

Selected publications:

RSV

• Genomic Sequencing Surveillance to Identify Respiratory Syncytial Virus Mutations, Arizona, USA. Holland LA, Holland SC, Smith MF, Leonard VR, Murugan V, Nordstrom L, Mulrow M, Salgado R, White M, Lim ES.

  Emerging Infectious Diseases (2023)

SARS-CoV-2

• Digital PCR discriminates between SARS-CoV-2 Omicron variants and immune escape mutations. Holland SC, Holland LA, Smith MF, MB Lee, Hu JC, Lim ES.

  Microbiology Spectrum (2023)

• Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA.  Smith MF, Holland SC, MB Lee, Hu JC, Pham NC, Sullins RA, Holland LA, Mu T, Thomas AW, Fitch R, Driver EM, Halden RU, Villegas-Gold M, Sanders S, Krauss JL, Nordstrom L, Mulrow M, White M, Murugan V, Lim ES.

  mBio (2023)

• SARS-CoV-2 Delta variant N gene mutations reduce sensitivity to the TaqPath COVID-19 multiplex molecular diagnostic assay. Holland SC, Bains A, Holland LA, Smith MF, Sullins RA, Mellor NJ, Thomas AW, Johnson N, Murugan V, Lim ES.

  Viruses (2022)

• University-Associated SARS-CoV-2 Omicron BA.2 Infections, Maricopa County, Arizona, USA, 2022. Fowle N, Garrett B, Floyd OL, Collins J, Krasnow AD, Islas M, Holland SC, Smith MF, Lim ES, Jarrett NM, Scott SE.

  Emerging Infectious Diseases (2022)

• Genomic Sequencing Surveillance Identifies Emergence of SARS-CoV-2 E484K variant B.1.243.1 in Arizona. Skidmore PT, Kaelin EA, Holland LA, Maqsood R, Wu LI, Mellor NJ, Blain JM, Harris V, LaBaer J, Murugan V, Lim ES.

  Emerging Infectious Diseases (2021)

• An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020). Holland LA, Kaelin EA, Maqsood R, Estifanos B, Wu LI, Varsani A, Halden RU, Hogue BG, Scotch M, Lim ES.

  Journal of Virology (2020)

Virome in Health and Disease

• Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants. Kaelin EA, Rodriguez C, Hall-Moore C, Hoffmann JA, Linneman LA, Ndao IM, Warner BB, Tarr PI, Holtz LR, Lim ES.

  Nature Microbiology (2022)

• Dynamic changes in breast milk microbiome in the early postpartum period of Kenyan women living with HIV are influenced by antibiotics but not antiretrovirals. Maqsood R, Skidmore PT, Holland LA, Au JL, Khan AK, Wu LI, Ma N, Begnel ER, Chohan BH, Adhiambo J, John-Stewart G, Kiarie J, Kinuthia J, Chung MH, Richardson BA, Slyker J, Lehman DA, Lim ES.

  Microbiology Spectrum (2022)

• Cervicovaginal DNA virome alterations are associated with genital inflammation and microbiota composition. Kaelin EA, Skidmore PT, Laniewski P, Holland LA, Chase DM, Herbst-Kralovetz MM, Lim ES.

  mSystems (2022)

• Breast milk virome and bacterial microbiome resilience in Kenyan women living with HIV.  Maqsood R, Reus JB, Wu LI, Holland LA, Nduati R, Mbori-Ngacha D, Maleche-Obimbo E, Begnel ER, Gantt S, Ojee E, Wamalwa D, John-Stewart G, Slyker J, Lehman DA, Lim ES.

  mSystems (2021)

• Discordant transmission of bacteria and viruses from mothers to babies at birth. Maqsood R, Rodgers R, Rodriguez C, Handley SA, Ndao IM, Tarr PI, Warner BB, Lim ES, Holtz LR.

  Microbiome (2019)