Local protocol repository

This section provides access to both spanish and english versions of our laboratory's standard operating procedures (SOPs). The Viral and Human Genomics Laboratory is committed to promoting the human rights of free access to knowledge and to receiving the benefits of scientific progress and its applications by providing universal access to all the resources and publications it produces. This is in agreement with article 15 of the United Nations International Covenant on Economic, Social and Cultural Rights published on April 30, 2020.

As such, this document is distributed under a Creative Commons Attribution 4.0 International (CC BY 4.0 DEED) license which grants the licensee (you) the right to copy, remix, transform, develop and redistribute the material in any medium or format for any purpose, including commercial purposes provided that 1) corresponding credit is given to the licensing author (us) as “Laboratory of Viral and Human Genomics, Faculty of Medicine UASLP”, 2) any changes to the original document are indicated and, 3) in no way suggest that the licensor endorses the derivative work.

All rights reserved © 2024 Laboratorio de Genómica Viral y Humana, Facultad de Medicina UASLP.

(Last updated: April 15, © 2024.)

Novel additions to our protocols

AED defibrillator verification checklist. (English), last update Apr 2024.

Primedic Defi-B defibrillator verification checklist. (English), last update Apr 2024.

Laboratory BSL-2 area verification checklist. (English, Español), last update Apr 2024.

Laboratory verification routine. (English, Español), last update Apr 2024.

A.- General laboratory procedures

1.- Operating the portable emergency power-plant. (English, Español), last update Nov 2023. Updated!

2.- Laboratory fire alarm operation. (English, Español), last update Nov 2023.

3.- Mexican Genomic DNA Collection (MGDC) sample referral and processing. (Español), last update Mar 2019.

4.- LGVH Biobank sample referral, processing and informed consent form. (Español), last update Mar 2020.

5.- Operating the tissue-culture incubator’s CO2 regulator. (English), last update Oct 2018.

6.- Cyberbiosecurity, Scanning USB drives for viruses. (English), last update Mar 2024.

7.- Laboratory verification routine. (English, Español), last update Apr 2024.

8.- Laboratory BSL-2 area verification checklist. (English, Español), last update Mar 2024.

9.- AED defibrillator verification checklist. (English), last update Apr 2024.

10.- Primedic Defi-B defibrillator verification checklist. (English), last update Apr 2024.

B.- Biosafety

1.- Human & Viral Genomics Laboratory Biosafety and Operations Manual, version 6 2020. (Español), last update Jan 2020.

2.- Human & Viral Genomics Laboratory biological risk assessment and plans. (Spanish), last update Feb 2022.

3.- Baseline serum processing and storage. (English), last update Mar 2021.

4.- Medical evaluation and follow-up form. (Spanish PDF) (Spanish DOCX), last update Feb 2022.

5.- Laboratory incident and spill report form (version 7). (Spanish), last update Oct 2022.

6.- Hand hygiene and handwash and self-assessment form. (English), last update Jun 2021.

7.- Confidentiality agreement. (Spanish), last update Feb 2022.

8.- Baseline serum informed consent form. (Spanish), last update Sep 2023.

9.- Biological safety cabinet (BSC) proficiency assessment form. (English), last update Mar 2022.

10.- N95 respirator fit test. (English), last update Mar 2021.

11.- N95 respirator fit test assessment form. (English), last update Jan 2021.

12.- BSL-2 biological decontamination procedure.(English), last update Mar 2021.

13.- Laboratory decontamination following COVID-19 sample RNA extraction. (English, Español), last update Sep 2021. Updated!

C.- BSL-3 operations

1.- BSL3 laboratory maintenance routine. (Español), last update. WORK IN PROGRESS

2.- Pre-BSL-3 medical evaluation assessment form. (Spanish PDF) (Spanish DOCX), last update Mar 2022.

3.- Donning of BSL-3 personal protective equipment (PAPR & Coverall). (English, Español), last update Jul 2023. Updated!

4.- BSL-3 biological decontamination procedure. (English), last update Mar 2021.

5.- Wild bat & rodent carcass decontamination. (English), last update Mar 2021.

D.- Cell biology

1.- Phosphate buffered saline (PBS) preparation. (Español), last update Apr 2008.

2.- Penicillin-Streptomycin (Pen-Strep) preparation. (Español), last update Nov 2008.

3.- Cyclosporin A preparation. (Español), last update Nov 2009.

4.- Viral transport media (VTM) preparation. (English), last update May 2017.

5.- Peripheral blood mononuclear cell isolation with ficoll. (Español), last update Nov 2013.

6.- Performing cell counts with haemocytometer. (English, Español), last update Oct 2013.

7.- EBV-transformation of peripheral blood mononuclear cells to B-lymphoblastoid cell lines (BLCLs). (Español), last update Mar 2021.

8.- B95-8 cell line thawing, expansion, supernatant collection and cryopreservation. (Español), last update Oct 2023.

9.- Cryopreservation of peripheral blood mononuclear cells. (Español), last update Nov 2013.

10.- PCR detection of Mycoplasma contamination. (Español), last update Nov 2013.

E.- Molecular biology

1.- Agarose gel electrophoresis of nucleic acids. (Español), last update Nov 2008.

2.- TAE & TBE electrophoresis buffer preparation. (English), last update May 2017.

3.- Electrophoresis loading-buffer preparation. (Español), last update Mar 2021.

4.- TE 10:1 buffer preparation. (Español), last update Nov 2008.

5.- Preparation of ethidium bromide for visualizing PCR products. (English, Español), last update Nov 2023.

6.- Ethidium bromide decontamination of electrophoresis buffers. (English), last update May 2017.

7.- In-house RNA stabilization solution. (English), last update Apr 2024.

8.- Reconstitution of oligonucleotide primers. (Español), last update May 2009.

9.- Drabek maxiprep DNA extraction from leukocyte concentrates. (English), last update Nov 2019.

10.- Drabek midiprep DNA extraction from whole-blood. (English), last update Nov 2019.

11.- Drabek miniprep DNA extraction from whole-blood. (English), last update Nov 2019.

12.- Drabek microprep DNA extraction from whole-blood. (English), last update Nov 2019.

13.- Drabek microprep DNA extraction from leukocyte concentrates. (English), last update Nov 2019.

14.- Phenol-chloroform DNA extraction from leukocyte concentrates. (Español), last update Jun 2014.

15.- Phenol-chloroform DNA extraction from peripheral blood mononuclear cells. (Español), last update Jun 2014.

16.- Viral RNA extraction using Roche's kit. (English), last update June 2018.

17.- Molecular decontamination of micropipettes and work surfaces. (English), last update Nov 2017.

18.- RT-PCR amplification of mammalian 18S rRNA. (English), last update Jul 2021.

19.- RNA extraction from wild small mammals using TRIzol in BSL3 discipline. (English), last update Mar 2021.

20.- Proteinase K DNA extraction from urine, blood serum or plasma. (English), last update Jun 2021.

21.- Using uMelt algorithm to predict fluorescent melting curves for the ABI7500. (English), last update June 2017.

F.- Human genomics

1.- Killer-cell Immunoglobulin-like Receptor (KIR) genotyping. (English), last update May 2017.

2.- CC-Chemokine receptor (CCR5)-delta32 genotyping. (English), last update May 2017.

3.- HLA-C group 1 and 2 KIR-ligand genotyping. (English), last update Mar 2015.

4.- HLA-Bw4 and Bw6 KIR-ligand genotyping. (English), last update. WORK IN PROGRESS

5.- HLA-C -35Kb single nucleotide polymorphism (rs9264942) genotyping. (English), last update May 2017.

6.- Human DNA authentication using Combined DNA Index System (CODIS) profiling. (English), last update May 2009.

G.- Blood-borne viral pathogens

1.- Multiplex PCR screening of HBV, HIV and CMV (English), last update Mar 2021.

2.- Hepatitis B Virus (HBV) detection by end-point PCR. (English), last update Mar 2021.

3.- Hepatitis B virus (HBV) detection & quantitation using qPCR (SYBR green). (English), last update Mar 2021.

4.- Hepatitis B virus (HBV) full-genomic amplification & sequencing. (English), last update Mar 2021.

5.- Hepatitis C Virus (HCV) detection by two-step end-point RT-PCR. (Español), last update Mar 2021.

6.- Hepatitis C Virus (HCV) detection and quantitation by qRT-PCR (SYBR green). (Español), last update Mar 2021.

7.- Human Immunodeficiency Virus (HIV) RNA detection by end-point RT-PCR. (Español), last update Mar 2021.

8.- Human Immunodeficiency Virus (HIV) proviral DNA detection by end-point RT-PCR. (Español), last update Mar 2021.

9.- Human Immunodeficiency Virus (HIV) detection & quantitation by qRT-PCR (Taqman). (English), last update Mar 2021.

10.- Human Immunodeficiency Virus (HIV) protease region amplification & sequencing. (English), last update Mar 2021.

11.- Human Immunodeficiency Virus (HIV) reverse transcriptase region amplification & sequencing. (English), last update Mar 2021.

12.- Human Immunodeficiency Virus (HIV) integrase region amplification & sequencing. (English), last update Mar 2021.

13.- Human Immunodeficiency Virus (HIV) vif region amplification & sequencing. (English), last update. WORK IN PROGRESS

14.- Human Cytomegalovirus (CMV) detection & quantitation by qPCR (SYBR Green format).(English), last update Mar 2021.

15.- Human Cytomegalovirus (CMV) detection & quantitation by qPCR (EVA Green format).(English), last update Mar 2021.

16.- GB virus C (GBV-C) detection by qRT-PCR. (English), last update. WORK IN PROGRESS

H.- Respiratory viral pathogens

1.- Pre-pandemic influenza virus A (H1N1) & (H3N2) full-genomic amplification & sequencing. (English, Español), last update Mar 2021.

2.- Pre-pandemic influenza virus A (H1N1), (H3N2) & (H5N1) subtyping by end-point RT-PCR. (Español), last update May 2009.

3.- Influenza virus A & B typing by end-point RT-PCR. (Español), last update Jun 2009.

4.- Pandemic influenza virus A (H1N1) full-genomic amplification & sequencing. (Español), last update Aug 2013.

5.- Pandemic influenza virus A (H1N1) detection by end-point RT-PCR. (Español), last update May 2009.

6.- SARS-Coronavirus (SARS-CoV-1) detection & quantitation by qRT-PCR (SYBR green). (English), last update Nov 2018.

7.- SARS-Coronavirus (SARS-CoV-1) confirmatory RdRp sequencing. (English), last update Nov 2017.

8.- MERS-Coronavirus (MERS-CoV) detection & quantitation by qRT-PCR (SYBR green). (English), last update Nov 2018.

9.- Hantavirus detection & quantitation by qRT-PCR (EvaGreen). (English), last update Oct 2017.

10.- COVID-19 sampling field station deployment. (English), last update Feb 2021.

11.- RNA extraction of COVID-19 suspected samples using QIAamp Viral RNA kit. (English, Español), last update Jun 2021. New!

12.- SARS-CoV-2 and Beta Coronavirus detection using GeneFinder RT-qPCR kit. (English), last update Jun 2021. New!

13.- SARS-CoV-2 detection using ScienCell RT-qPCR kit. (English), last update Sep 2021. New!

I.- Arthropod-borne viral pathogens (Arbovirus)

1.- Yoy mosquito trap construction. (English), last update Sep 2021.

2.- Yoy mosquito trap construction diagram. (English), last update Sep 2021.

3.- Yoy mosquito trap mesh funnel template. (English), last update Sep 2021.

4.- Yoy mosquito trap assembly. (English), last update Sep 2021.

5.- Yoy mosquito trap assembly diagram. (English), last update Sep 2021.

6.- Preparation of honey saturated FTA cards for YOY mosquito traps. (English), (Español), last update. WORK IN PROGRESS

7.- Field deployment of Yoy mosquito traps. (English), (Español), last update. WORK IN PROGRESS

8.- Phenol-Chloroform-Isoamyl alcohol extraction of mosquito DNA. (English), last update May 2019.

9.- Drabek microprep extraction of mosquito DNA. (English), last update Jun 2019.

10.- Molecular taxonomy of mosquitoes through endpoint PCR. (English), last update May 2022.

11.- Dengue virus (DENV) detection & quantitation by qRT-PCR. (English), last update Nov 2018.

12.- Dengue virus (DENV) subtyping by end-point RT-PCR. (English), last update Apr 2021.

13.- West Nile Virus (WNV) detection & quantitation by qRT-PCR (SYBR/EVAgreen). (English), last update Jul 2017.

14.- Zika virus (ZIKV) detection & quantitation by qRT-PCR. (English), last update Jul 2017.

15.- Chikungunya virus (CHIKV) detection & quantitation by qRT-PCR. (English), last update. WORK IN PROGRESS

J.- Rodent and Bat-borne viral pathogens

1.- Expedition checklist for bat and rodent collections. (English), last update. WORK IN PROGRESS

2.- Wild bat & rodent capture, handling and field-work. (English), last update Jul 2017.

3.- Wild bat & rodent necropsy and sample collection. (English), last update Jul 2017.

4.- RNA extraction from wild small mammals using TRIzol in BSL3 discipline. (English), last update Mar 2021.

5.- Hantavirus (HNT) detection & quantitation by qRT-PCR (EVAgreen). (English), last update Oct 2017.

6.- Hantavirus (HNT) detection & quantitation by qRT-PCR (Taqman). (English), last update. PENDING

7.- Wild bat & rodent carcass decontamination. (English), last update Mar 2021.

8.- Suspected rabies (RABV) specimen handling, transport and processing. (English), last update Jul 2017.

9.- Rabies virus (RABV) detection & quantitation by qRT-PCR (SYBR Green). (English), last update Jun 2017.

10.- Rabies virus (RABV) isolation and culture. (English), last update Mar 2021.

11.- Rabies immunofluorescence test request form. (Español), last update Mar 2021.

12.- Rabies immunofluorescence test report form. (Español), last update Mar 2021.

13.- SARS-Coronavirus (SARS-CoV-1) detection & quantitation by qRT-PCR (SYBR green). (English), last update Nov 2018.

14.- SARS-Coronavirus (SARS-CoV-1) confirmatory RdRp sequencing. (English), last update Nov 2017.

15.- MERS-Coronavirus (MERS-CoV) detection & quantitation by qRT-PCR (SYBR green). (English), last update Nov 2018.

16.- Human anti-hantavirus antibody detection through ELISA. (English, Spanish), last update Apr 2024.

K.- Multimedia Protocols in Bioscience

1.- Exotic viral pathogen surveillance in Mexican bat populations.
2.- Haematophagus (vampire) bat processing for viral pathogen screening.
3.- UASLP emerging viral pathogen surveillance network.
4- Biocontainment laboratory entry and exit procedure.
5- Working in class II A2 biological safety cabinets.
6.- Airflow patterns in biological safety cabinets and laminar flow hoods.
7.- Isolation of peripheral blood mononuclear cells using ficoll-1077.
8.- Generating B-lymphoblastoid cell lines using Epstein Barr virus transformation.
9.- B-lymphoblastoid cell line morphology through phase-contrast microscope.
10.- Thawing of cryopreserved peripheral blood mononuclear cells or cell lines.
11.- Spectrophotometric evaluation of DNA using a Nanodrop ND-1000.
12.- Drabek genomic DNA extractions from peripheral blood.
13.- Molecular discipline while preparing real time PCR assays.
14.- Ethidium bromide decontamination/reclamation of elecptrophoresis buffers.
15.- Virtual tour through the Viral & Human Genomics Lab version 2.0 (2016).
16.- PrimerDesign Genesig Q16 portable real-time thermal cycler.
17.- Velab VE-146YT epifluorescence compound microscope assembly.
18.- Velab VE-146YT epifluorescence compound microscope use.
19.- Thermo Scientific NanoDrop One microvolumetric spectrophotometer..
20.- Thermo Fisher Ultra-Low Revco (-80ºC) vertical freezers.
21.- AppliedBiosystem's MiniAmp Plus end-point gradient thermal cycler.
22.- COVID-19 prevention, mexican sign language.
23.- COVID-19 sampling field station layout.
24.- Emerging Viral Pathogen Surveillance Workgroup (RVPVE) - Gruta la Catedral.
25.- Field station COVID-19 sampling station (UASLP Proyecto Virus) - Ladrilleras Tercera Sección.
26.- 2023 Viral & Human Genomics BSL-3 facility promotional video.